mant amppnp  (Jena Bioscience)


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    Name:
    Mant AMP
    Description:

    Catalog Number:
    NU-236L
    Price:
    369.6
    Category:
    Nucleotides Nucleosides
    Size:
    5 x 150 µl
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    Structured Review

    Jena Bioscience mant amppnp
    Atomic Model of the MDA5-dsRNA Filament (A) Domain structure of mouse MDA5. CARD, caspase recruitment domain; CTD, C-terminal domain; Hel1 and Hel2, first and second RecA-like helicase domains; Hel2i, Hel2 insert domain; P, pincer domain. The same color code and domain abbreviations are used in subsequent panels and in Figures 1 , 7A, and 7 D. (B) Overview of the refined atomic model of the MDA5-dsRNA filament. Two adjacent MDA5 subunits and 28 bp of dsRNA are shown from the Twist74 structure. <t>RNA</t> is in magenta. The bound <t>AMPPNP</t> molecules are shown in sphere representation. The two filament-forming interfaces are boxed. (C and D) Close-up views of filament interface II (C) and interface I (D). The top panels show side chains forming key contacts, with hydrogen bonds shown as yellow dashed lines. In the middle panels the lower protomer in (B) is shown in surface representation colored by hydrophobicity from gray to green, with green being the most hydrophobic. In the lower panels, the upper protomer in (B) is shown in surface representation colored by hydrophobicity. The orientation of the view relative to (B) is indicated for each panel. See also Figure S3 and Videos S1 , S2 , S3 , S4 , and S5 .

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    Images

    1) Product Images from "Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis"

    Article Title: Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis

    Journal: Molecular Cell

    doi: 10.1016/j.molcel.2018.10.012

    Atomic Model of the MDA5-dsRNA Filament (A) Domain structure of mouse MDA5. CARD, caspase recruitment domain; CTD, C-terminal domain; Hel1 and Hel2, first and second RecA-like helicase domains; Hel2i, Hel2 insert domain; P, pincer domain. The same color code and domain abbreviations are used in subsequent panels and in Figures 1 , 7A, and 7 D. (B) Overview of the refined atomic model of the MDA5-dsRNA filament. Two adjacent MDA5 subunits and 28 bp of dsRNA are shown from the Twist74 structure. RNA is in magenta. The bound AMPPNP molecules are shown in sphere representation. The two filament-forming interfaces are boxed. (C and D) Close-up views of filament interface II (C) and interface I (D). The top panels show side chains forming key contacts, with hydrogen bonds shown as yellow dashed lines. In the middle panels the lower protomer in (B) is shown in surface representation colored by hydrophobicity from gray to green, with green being the most hydrophobic. In the lower panels, the upper protomer in (B) is shown in surface representation colored by hydrophobicity. The orientation of the view relative to (B) is indicated for each panel. See also Figure S3 and Videos S1 , S2 , S3 , S4 , and S5 .
    Figure Legend Snippet: Atomic Model of the MDA5-dsRNA Filament (A) Domain structure of mouse MDA5. CARD, caspase recruitment domain; CTD, C-terminal domain; Hel1 and Hel2, first and second RecA-like helicase domains; Hel2i, Hel2 insert domain; P, pincer domain. The same color code and domain abbreviations are used in subsequent panels and in Figures 1 , 7A, and 7 D. (B) Overview of the refined atomic model of the MDA5-dsRNA filament. Two adjacent MDA5 subunits and 28 bp of dsRNA are shown from the Twist74 structure. RNA is in magenta. The bound AMPPNP molecules are shown in sphere representation. The two filament-forming interfaces are boxed. (C and D) Close-up views of filament interface II (C) and interface I (D). The top panels show side chains forming key contacts, with hydrogen bonds shown as yellow dashed lines. In the middle panels the lower protomer in (B) is shown in surface representation colored by hydrophobicity from gray to green, with green being the most hydrophobic. In the lower panels, the upper protomer in (B) is shown in surface representation colored by hydrophobicity. The orientation of the view relative to (B) is indicated for each panel. See also Figure S3 and Videos S1 , S2 , S3 , S4 , and S5 .

    Techniques Used:

    Cryo-EM Image Reconstruction of MDA5-dsRNA Filaments with Helical Symmetry Averaging (A) Representative cryo-EM micrograph of MDA5-dsRNA filaments. (B) Cryo-EM micrograph shown in (A) with circles drawn around the boxed filament segments that were used in the helical reconstructions. The circles are colored according to the 3D class that they contributed to. Segments that contributed to the Twist74, Twist87, and Twist91 structures are in red, green, and blue, respectively. (C) Histogram showing the distributions of filament segments as a function of helical twist for the ATP, ADP-AlF 4 , 1-mM AMPPNP, and nucleotide-free datasets. The distributions shown are from 3D classification performed with ten classes per dataset. Error bars represent SEM between replicate 3D classification calculations; n = 3. (D) 3D density map of the Twist74 MDA5-dsRNA filament at 3.68 Å overall resolution. The components are colored as follows: Hel1, green; Hel2, cyan; Hel2i, yellow; pincer domain, red; CTD, orange; and RNA, magenta. (E) The dsRNA density in the Twist74 filament (blue mesh) is shown with the fitted atomic model (magenta and pink). See also Figures S1 and S2 .
    Figure Legend Snippet: Cryo-EM Image Reconstruction of MDA5-dsRNA Filaments with Helical Symmetry Averaging (A) Representative cryo-EM micrograph of MDA5-dsRNA filaments. (B) Cryo-EM micrograph shown in (A) with circles drawn around the boxed filament segments that were used in the helical reconstructions. The circles are colored according to the 3D class that they contributed to. Segments that contributed to the Twist74, Twist87, and Twist91 structures are in red, green, and blue, respectively. (C) Histogram showing the distributions of filament segments as a function of helical twist for the ATP, ADP-AlF 4 , 1-mM AMPPNP, and nucleotide-free datasets. The distributions shown are from 3D classification performed with ten classes per dataset. Error bars represent SEM between replicate 3D classification calculations; n = 3. (D) 3D density map of the Twist74 MDA5-dsRNA filament at 3.68 Å overall resolution. The components are colored as follows: Hel1, green; Hel2, cyan; Hel2i, yellow; pincer domain, red; CTD, orange; and RNA, magenta. (E) The dsRNA density in the Twist74 filament (blue mesh) is shown with the fitted atomic model (magenta and pink). See also Figures S1 and S2 .

    Techniques Used:

    2) Product Images from "Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis"

    Article Title: Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis

    Journal: Molecular Cell

    doi: 10.1016/j.molcel.2018.10.012

    Atomic Model of the MDA5-dsRNA Filament (A) Domain structure of mouse MDA5. CARD, caspase recruitment domain; CTD, C-terminal domain; Hel1 and Hel2, first and second RecA-like helicase domains; Hel2i, Hel2 insert domain; P, pincer domain. The same color code and domain abbreviations are used in subsequent panels and in Figures 1 , 7A, and 7 D. (B) Overview of the refined atomic model of the MDA5-dsRNA filament. Two adjacent MDA5 subunits and 28 bp of dsRNA are shown from the Twist74 structure. RNA is in magenta. The bound AMPPNP molecules are shown in sphere representation. The two filament-forming interfaces are boxed. (C and D) Close-up views of filament interface II (C) and interface I (D). The top panels show side chains forming key contacts, with hydrogen bonds shown as yellow dashed lines. In the middle panels the lower protomer in (B) is shown in surface representation colored by hydrophobicity from gray to green, with green being the most hydrophobic. In the lower panels, the upper protomer in (B) is shown in surface representation colored by hydrophobicity. The orientation of the view relative to (B) is indicated for each panel. See also Figure S3 and Videos S1 , S2 , S3 , S4 , and S5 .
    Figure Legend Snippet: Atomic Model of the MDA5-dsRNA Filament (A) Domain structure of mouse MDA5. CARD, caspase recruitment domain; CTD, C-terminal domain; Hel1 and Hel2, first and second RecA-like helicase domains; Hel2i, Hel2 insert domain; P, pincer domain. The same color code and domain abbreviations are used in subsequent panels and in Figures 1 , 7A, and 7 D. (B) Overview of the refined atomic model of the MDA5-dsRNA filament. Two adjacent MDA5 subunits and 28 bp of dsRNA are shown from the Twist74 structure. RNA is in magenta. The bound AMPPNP molecules are shown in sphere representation. The two filament-forming interfaces are boxed. (C and D) Close-up views of filament interface II (C) and interface I (D). The top panels show side chains forming key contacts, with hydrogen bonds shown as yellow dashed lines. In the middle panels the lower protomer in (B) is shown in surface representation colored by hydrophobicity from gray to green, with green being the most hydrophobic. In the lower panels, the upper protomer in (B) is shown in surface representation colored by hydrophobicity. The orientation of the view relative to (B) is indicated for each panel. See also Figure S3 and Videos S1 , S2 , S3 , S4 , and S5 .

    Techniques Used:

    Comparison of the Closed ADP-AlF 4 -Bound Structure with the Semi-open Structures and Schematic Model of the ATPase Cycle and Proofreading Mechanism of MDA5 For a Figure360 author presentation of Figure 7, see https://doi.org/10.1016/j.molcel.2018.10.012 . (A) Close-up view of the nucleotide-binding site and Hel1-Hel2 domain interface. The Twist74 AMPPNP-bound structure (blue) was superimposed on the ADP-AlF 4 -bound structure (colored by domain as in Figure 2 ) using the Hel1 domain as the reference. Nucleotide-binding motifs Va and VI are labeled. Only the ADP-AlF 4 nucleotide is shown for clarity. (B) Close-up view of the Hel2-loop and its interactions with the dsRNA. The Twist74 (blue) and Twist87 (pink) AMPPNP-bound structures are superimposed onto the ADP-AlF 4 -bound structure (green) using Hel1 as the reference. (C) Overview of Twist74 (blue) superimposed on the ADP-AlF 4 -bound structure (green) using Hel1 as the reference. (D) Model of the ATPase cycle and proofreading mechanism. Only two filament protomers are shown for clarity. The low-twist (71°–81°) structures correspond to the ATP-bound catalytic ground state, the intermediate-twist (81°–91°) ADP-AlF 4 -bound structure is the transition state, and the intermediate- and high-twist (91°–96°) states represent nucleotide-free states. The four panels relate to the panels in Figures 3 C–3F. See also Videos S1 , S2 , S3 , S4 , and S5 . Figure360: An Author Presentation of Figure 7
    Figure Legend Snippet: Comparison of the Closed ADP-AlF 4 -Bound Structure with the Semi-open Structures and Schematic Model of the ATPase Cycle and Proofreading Mechanism of MDA5 For a Figure360 author presentation of Figure 7, see https://doi.org/10.1016/j.molcel.2018.10.012 . (A) Close-up view of the nucleotide-binding site and Hel1-Hel2 domain interface. The Twist74 AMPPNP-bound structure (blue) was superimposed on the ADP-AlF 4 -bound structure (colored by domain as in Figure 2 ) using the Hel1 domain as the reference. Nucleotide-binding motifs Va and VI are labeled. Only the ADP-AlF 4 nucleotide is shown for clarity. (B) Close-up view of the Hel2-loop and its interactions with the dsRNA. The Twist74 (blue) and Twist87 (pink) AMPPNP-bound structures are superimposed onto the ADP-AlF 4 -bound structure (green) using Hel1 as the reference. (C) Overview of Twist74 (blue) superimposed on the ADP-AlF 4 -bound structure (green) using Hel1 as the reference. (D) Model of the ATPase cycle and proofreading mechanism. Only two filament protomers are shown for clarity. The low-twist (71°–81°) structures correspond to the ATP-bound catalytic ground state, the intermediate-twist (81°–91°) ADP-AlF 4 -bound structure is the transition state, and the intermediate- and high-twist (91°–96°) states represent nucleotide-free states. The four panels relate to the panels in Figures 3 C–3F. See also Videos S1 , S2 , S3 , S4 , and S5 . Figure360: An Author Presentation of Figure 7

    Techniques Used: Binding Assay, Labeling

    Cryo-EM Image Reconstruction of MDA5-dsRNA Filaments with Helical Symmetry Averaging (A) Representative cryo-EM micrograph of MDA5-dsRNA filaments. (B) Cryo-EM micrograph shown in (A) with circles drawn around the boxed filament segments that were used in the helical reconstructions. The circles are colored according to the 3D class that they contributed to. Segments that contributed to the Twist74, Twist87, and Twist91 structures are in red, green, and blue, respectively. (C) Histogram showing the distributions of filament segments as a function of helical twist for the ATP, ADP-AlF 4 , 1-mM AMPPNP, and nucleotide-free datasets. The distributions shown are from 3D classification performed with ten classes per dataset. Error bars represent SEM between replicate 3D classification calculations; n = 3. (D) 3D density map of the Twist74 MDA5-dsRNA filament at 3.68 Å overall resolution. The components are colored as follows: Hel1, green; Hel2, cyan; Hel2i, yellow; pincer domain, red; CTD, orange; and RNA, magenta. (E) The dsRNA density in the Twist74 filament (blue mesh) is shown with the fitted atomic model (magenta and pink). See also Figures S1 and S2 .
    Figure Legend Snippet: Cryo-EM Image Reconstruction of MDA5-dsRNA Filaments with Helical Symmetry Averaging (A) Representative cryo-EM micrograph of MDA5-dsRNA filaments. (B) Cryo-EM micrograph shown in (A) with circles drawn around the boxed filament segments that were used in the helical reconstructions. The circles are colored according to the 3D class that they contributed to. Segments that contributed to the Twist74, Twist87, and Twist91 structures are in red, green, and blue, respectively. (C) Histogram showing the distributions of filament segments as a function of helical twist for the ATP, ADP-AlF 4 , 1-mM AMPPNP, and nucleotide-free datasets. The distributions shown are from 3D classification performed with ten classes per dataset. Error bars represent SEM between replicate 3D classification calculations; n = 3. (D) 3D density map of the Twist74 MDA5-dsRNA filament at 3.68 Å overall resolution. The components are colored as follows: Hel1, green; Hel2, cyan; Hel2i, yellow; pincer domain, red; CTD, orange; and RNA, magenta. (E) The dsRNA density in the Twist74 filament (blue mesh) is shown with the fitted atomic model (magenta and pink). See also Figures S1 and S2 .

    Techniques Used:

    Interface Mutations that Impair Signaling Also Impair Filament Formation (A) Representative electron micrographs of MDA5 filament interface mutants in the presence of 1 kb dsRNA, 1 mM AMPPNP, and 5 mM MgCl 2 . Scale bars, 100 nm. Residue numbers refer to mouse MDA5. (B) Table summarizing the filament formation activity, filament length, cell-signaling activity, and ATPase activity of selected MDA5 mutants. ATPase activities were calculated from the initial slopes of the curves in Figure 5 D and is expressed as moles of released phosphate per mole of MDA5 per second (M Pi M MDA5 −1 s −1 ). Residue numbers refer to mouse MDA5. For mutants with different residue numbers in human MDA5, the corresponding mutation is shown in human residue numbers at the bottom. n.d., not determined. See also Figures S5 and S7 .
    Figure Legend Snippet: Interface Mutations that Impair Signaling Also Impair Filament Formation (A) Representative electron micrographs of MDA5 filament interface mutants in the presence of 1 kb dsRNA, 1 mM AMPPNP, and 5 mM MgCl 2 . Scale bars, 100 nm. Residue numbers refer to mouse MDA5. (B) Table summarizing the filament formation activity, filament length, cell-signaling activity, and ATPase activity of selected MDA5 mutants. ATPase activities were calculated from the initial slopes of the curves in Figure 5 D and is expressed as moles of released phosphate per mole of MDA5 per second (M Pi M MDA5 −1 s −1 ). Residue numbers refer to mouse MDA5. For mutants with different residue numbers in human MDA5, the corresponding mutation is shown in human residue numbers at the bottom. n.d., not determined. See also Figures S5 and S7 .

    Techniques Used: Activity Assay, Mutagenesis

    3) Product Images from "Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis"

    Article Title: Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis

    Journal: Molecular Cell

    doi: 10.1016/j.molcel.2018.10.012

    Atomic Model of the MDA5-dsRNA Filament (A) Domain structure of mouse MDA5. CARD, caspase recruitment domain; CTD, C-terminal domain; Hel1 and Hel2, first and second RecA-like helicase domains; Hel2i, Hel2 insert domain; P, pincer domain. The same color code and domain abbreviations are used in subsequent panels and in Figures 1 , 7A, and 7 D. (B) Overview of the refined atomic model of the MDA5-dsRNA filament. Two adjacent MDA5 subunits and 28 bp of dsRNA are shown from the Twist74 structure. RNA is in magenta. The bound AMPPNP molecules are shown in sphere representation. The two filament-forming interfaces are boxed. (C and D) Close-up views of filament interface II (C) and interface I (D). The top panels show side chains forming key contacts, with hydrogen bonds shown as yellow dashed lines. In the middle panels the lower protomer in (B) is shown in surface representation colored by hydrophobicity from gray to green, with green being the most hydrophobic. In the lower panels, the upper protomer in (B) is shown in surface representation colored by hydrophobicity. The orientation of the view relative to (B) is indicated for each panel. See also Figure S3 and Videos S1 , S2 , S3 , S4 , and S5 .
    Figure Legend Snippet: Atomic Model of the MDA5-dsRNA Filament (A) Domain structure of mouse MDA5. CARD, caspase recruitment domain; CTD, C-terminal domain; Hel1 and Hel2, first and second RecA-like helicase domains; Hel2i, Hel2 insert domain; P, pincer domain. The same color code and domain abbreviations are used in subsequent panels and in Figures 1 , 7A, and 7 D. (B) Overview of the refined atomic model of the MDA5-dsRNA filament. Two adjacent MDA5 subunits and 28 bp of dsRNA are shown from the Twist74 structure. RNA is in magenta. The bound AMPPNP molecules are shown in sphere representation. The two filament-forming interfaces are boxed. (C and D) Close-up views of filament interface II (C) and interface I (D). The top panels show side chains forming key contacts, with hydrogen bonds shown as yellow dashed lines. In the middle panels the lower protomer in (B) is shown in surface representation colored by hydrophobicity from gray to green, with green being the most hydrophobic. In the lower panels, the upper protomer in (B) is shown in surface representation colored by hydrophobicity. The orientation of the view relative to (B) is indicated for each panel. See also Figure S3 and Videos S1 , S2 , S3 , S4 , and S5 .

    Techniques Used:

    Comparison of the Closed ADP-AlF 4 -Bound Structure with the Semi-open Structures and Schematic Model of the ATPase Cycle and Proofreading Mechanism of MDA5 For a Figure360 author presentation of Figure 7, see https://doi.org/10.1016/j.molcel.2018.10.012 . (A) Close-up view of the nucleotide-binding site and Hel1-Hel2 domain interface. The Twist74 AMPPNP-bound structure (blue) was superimposed on the ADP-AlF 4 -bound structure (colored by domain as in Figure 2 ) using the Hel1 domain as the reference. Nucleotide-binding motifs Va and VI are labeled. Only the ADP-AlF 4 nucleotide is shown for clarity. (B) Close-up view of the Hel2-loop and its interactions with the dsRNA. The Twist74 (blue) and Twist87 (pink) AMPPNP-bound structures are superimposed onto the ADP-AlF 4 -bound structure (green) using Hel1 as the reference. (C) Overview of Twist74 (blue) superimposed on the ADP-AlF 4 -bound structure (green) using Hel1 as the reference. (D) Model of the ATPase cycle and proofreading mechanism. Only two filament protomers are shown for clarity. The low-twist (71°–81°) structures correspond to the ATP-bound catalytic ground state, the intermediate-twist (81°–91°) ADP-AlF 4 -bound structure is the transition state, and the intermediate- and high-twist (91°–96°) states represent nucleotide-free states. The four panels relate to the panels in Figures 3 C–3F. See also Videos S1 , S2 , S3 , S4 , and S5 . Figure360: An Author Presentation of Figure 7
    Figure Legend Snippet: Comparison of the Closed ADP-AlF 4 -Bound Structure with the Semi-open Structures and Schematic Model of the ATPase Cycle and Proofreading Mechanism of MDA5 For a Figure360 author presentation of Figure 7, see https://doi.org/10.1016/j.molcel.2018.10.012 . (A) Close-up view of the nucleotide-binding site and Hel1-Hel2 domain interface. The Twist74 AMPPNP-bound structure (blue) was superimposed on the ADP-AlF 4 -bound structure (colored by domain as in Figure 2 ) using the Hel1 domain as the reference. Nucleotide-binding motifs Va and VI are labeled. Only the ADP-AlF 4 nucleotide is shown for clarity. (B) Close-up view of the Hel2-loop and its interactions with the dsRNA. The Twist74 (blue) and Twist87 (pink) AMPPNP-bound structures are superimposed onto the ADP-AlF 4 -bound structure (green) using Hel1 as the reference. (C) Overview of Twist74 (blue) superimposed on the ADP-AlF 4 -bound structure (green) using Hel1 as the reference. (D) Model of the ATPase cycle and proofreading mechanism. Only two filament protomers are shown for clarity. The low-twist (71°–81°) structures correspond to the ATP-bound catalytic ground state, the intermediate-twist (81°–91°) ADP-AlF 4 -bound structure is the transition state, and the intermediate- and high-twist (91°–96°) states represent nucleotide-free states. The four panels relate to the panels in Figures 3 C–3F. See also Videos S1 , S2 , S3 , S4 , and S5 . Figure360: An Author Presentation of Figure 7

    Techniques Used: Binding Assay, Labeling

    Cryo-EM Image Reconstruction of MDA5-dsRNA Filaments with Helical Symmetry Averaging (A) Representative cryo-EM micrograph of MDA5-dsRNA filaments. (B) Cryo-EM micrograph shown in (A) with circles drawn around the boxed filament segments that were used in the helical reconstructions. The circles are colored according to the 3D class that they contributed to. Segments that contributed to the Twist74, Twist87, and Twist91 structures are in red, green, and blue, respectively. (C) Histogram showing the distributions of filament segments as a function of helical twist for the ATP, ADP-AlF 4 , 1-mM AMPPNP, and nucleotide-free datasets. The distributions shown are from 3D classification performed with ten classes per dataset. Error bars represent SEM between replicate 3D classification calculations; n = 3. (D) 3D density map of the Twist74 MDA5-dsRNA filament at 3.68 Å overall resolution. The components are colored as follows: Hel1, green; Hel2, cyan; Hel2i, yellow; pincer domain, red; CTD, orange; and RNA, magenta. (E) The dsRNA density in the Twist74 filament (blue mesh) is shown with the fitted atomic model (magenta and pink). See also Figures S1 and S2 .
    Figure Legend Snippet: Cryo-EM Image Reconstruction of MDA5-dsRNA Filaments with Helical Symmetry Averaging (A) Representative cryo-EM micrograph of MDA5-dsRNA filaments. (B) Cryo-EM micrograph shown in (A) with circles drawn around the boxed filament segments that were used in the helical reconstructions. The circles are colored according to the 3D class that they contributed to. Segments that contributed to the Twist74, Twist87, and Twist91 structures are in red, green, and blue, respectively. (C) Histogram showing the distributions of filament segments as a function of helical twist for the ATP, ADP-AlF 4 , 1-mM AMPPNP, and nucleotide-free datasets. The distributions shown are from 3D classification performed with ten classes per dataset. Error bars represent SEM between replicate 3D classification calculations; n = 3. (D) 3D density map of the Twist74 MDA5-dsRNA filament at 3.68 Å overall resolution. The components are colored as follows: Hel1, green; Hel2, cyan; Hel2i, yellow; pincer domain, red; CTD, orange; and RNA, magenta. (E) The dsRNA density in the Twist74 filament (blue mesh) is shown with the fitted atomic model (magenta and pink). See also Figures S1 and S2 .

    Techniques Used:

    Interface Mutations that Impair Signaling Also Impair Filament Formation (A) Representative electron micrographs of MDA5 filament interface mutants in the presence of 1 kb dsRNA, 1 mM AMPPNP, and 5 mM MgCl 2 . Scale bars, 100 nm. Residue numbers refer to mouse MDA5. (B) Table summarizing the filament formation activity, filament length, cell-signaling activity, and ATPase activity of selected MDA5 mutants. ATPase activities were calculated from the initial slopes of the curves in Figure 5 D and is expressed as moles of released phosphate per mole of MDA5 per second (M Pi M MDA5 −1 s −1 ). Residue numbers refer to mouse MDA5. For mutants with different residue numbers in human MDA5, the corresponding mutation is shown in human residue numbers at the bottom. n.d., not determined. See also Figures S5 and S7 .
    Figure Legend Snippet: Interface Mutations that Impair Signaling Also Impair Filament Formation (A) Representative electron micrographs of MDA5 filament interface mutants in the presence of 1 kb dsRNA, 1 mM AMPPNP, and 5 mM MgCl 2 . Scale bars, 100 nm. Residue numbers refer to mouse MDA5. (B) Table summarizing the filament formation activity, filament length, cell-signaling activity, and ATPase activity of selected MDA5 mutants. ATPase activities were calculated from the initial slopes of the curves in Figure 5 D and is expressed as moles of released phosphate per mole of MDA5 per second (M Pi M MDA5 −1 s −1 ). Residue numbers refer to mouse MDA5. For mutants with different residue numbers in human MDA5, the corresponding mutation is shown in human residue numbers at the bottom. n.d., not determined. See also Figures S5 and S7 .

    Techniques Used: Activity Assay, Mutagenesis

    Related Articles

    Mutagenesis:

    Article Title: Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis
    Article Snippet: 10 μM Mant-AMPPNP was selected for the assay as it was the minimum concentration required for detection of fluorescent signal relative to a blank containing 10 μM (1.14 g l−1 ) MDA5 and 0.303 g l−1 poly(I:C) RNA but no Mant-AMPPNP. .. Mouse MDA5 protein (WT or ATPase-defective mutant) was titrated from 0 to 40 μM into a solution containing 10 μM Mant-AMPPNP and poly(I:C) RNA at a 1:3 molar ratio of MDA5 to RNA binding sites, assuming 15 bp per binding site. ..

    RNA Binding Assay:

    Article Title: Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis
    Article Snippet: 10 μM Mant-AMPPNP was selected for the assay as it was the minimum concentration required for detection of fluorescent signal relative to a blank containing 10 μM (1.14 g l−1 ) MDA5 and 0.303 g l−1 poly(I:C) RNA but no Mant-AMPPNP. .. Mouse MDA5 protein (WT or ATPase-defective mutant) was titrated from 0 to 40 μM into a solution containing 10 μM Mant-AMPPNP and poly(I:C) RNA at a 1:3 molar ratio of MDA5 to RNA binding sites, assuming 15 bp per binding site. ..

    Binding Assay:

    Article Title: Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis
    Article Snippet: 10 μM Mant-AMPPNP was selected for the assay as it was the minimum concentration required for detection of fluorescent signal relative to a blank containing 10 μM (1.14 g l−1 ) MDA5 and 0.303 g l−1 poly(I:C) RNA but no Mant-AMPPNP. .. Mouse MDA5 protein (WT or ATPase-defective mutant) was titrated from 0 to 40 μM into a solution containing 10 μM Mant-AMPPNP and poly(I:C) RNA at a 1:3 molar ratio of MDA5 to RNA binding sites, assuming 15 bp per binding site. ..

    other:

    Article Title: Molecular Mechanisms of Allosteric Inhibition of Brain Glycogen Phosphorylase by Neurotoxic Dithiocarbamate Chemicals *
    Article Snippet: Mant-AMP was purchased from Jena Bioscience.

    Concentration Assay:

    Article Title: Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis
    Article Snippet: Concentrations of 0.2 μM, 2 μM 10 μM and 20 μM Mant-AMPPNP (Jena Bioscience) were tested for fluorescent signal. .. 10 μM Mant-AMPPNP was selected for the assay as it was the minimum concentration required for detection of fluorescent signal relative to a blank containing 10 μM (1.14 g l−1 ) MDA5 and 0.303 g l−1 poly(I:C) RNA but no Mant-AMPPNP. .. Mouse MDA5 protein (WT or ATPase-defective mutant) was titrated from 0 to 40 μM into a solution containing 10 μM Mant-AMPPNP and poly(I:C) RNA at a 1:3 molar ratio of MDA5 to RNA binding sites, assuming 15 bp per binding site.

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    Jena Bioscience mant amppnp
    Atomic Model of the MDA5-dsRNA Filament (A) Domain structure of mouse MDA5. CARD, caspase recruitment domain; CTD, C-terminal domain; Hel1 and Hel2, first and second RecA-like helicase domains; Hel2i, Hel2 insert domain; P, pincer domain. The same color code and domain abbreviations are used in subsequent panels and in Figures 1 , 7A, and 7 D. (B) Overview of the refined atomic model of the MDA5-dsRNA filament. Two adjacent MDA5 subunits and 28 bp of dsRNA are shown from the Twist74 structure. <t>RNA</t> is in magenta. The bound <t>AMPPNP</t> molecules are shown in sphere representation. The two filament-forming interfaces are boxed. (C and D) Close-up views of filament interface II (C) and interface I (D). The top panels show side chains forming key contacts, with hydrogen bonds shown as yellow dashed lines. In the middle panels the lower protomer in (B) is shown in surface representation colored by hydrophobicity from gray to green, with green being the most hydrophobic. In the lower panels, the upper protomer in (B) is shown in surface representation colored by hydrophobicity. The orientation of the view relative to (B) is indicated for each panel. See also Figure S3 and Videos S1 , S2 , S3 , S4 , and S5 .
    Mant Amppnp, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Atomic Model of the MDA5-dsRNA Filament (A) Domain structure of mouse MDA5. CARD, caspase recruitment domain; CTD, C-terminal domain; Hel1 and Hel2, first and second RecA-like helicase domains; Hel2i, Hel2 insert domain; P, pincer domain. The same color code and domain abbreviations are used in subsequent panels and in Figures 1 , 7A, and 7 D. (B) Overview of the refined atomic model of the MDA5-dsRNA filament. Two adjacent MDA5 subunits and 28 bp of dsRNA are shown from the Twist74 structure. RNA is in magenta. The bound AMPPNP molecules are shown in sphere representation. The two filament-forming interfaces are boxed. (C and D) Close-up views of filament interface II (C) and interface I (D). The top panels show side chains forming key contacts, with hydrogen bonds shown as yellow dashed lines. In the middle panels the lower protomer in (B) is shown in surface representation colored by hydrophobicity from gray to green, with green being the most hydrophobic. In the lower panels, the upper protomer in (B) is shown in surface representation colored by hydrophobicity. The orientation of the view relative to (B) is indicated for each panel. See also Figure S3 and Videos S1 , S2 , S3 , S4 , and S5 .

    Journal: Molecular Cell

    Article Title: Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis

    doi: 10.1016/j.molcel.2018.10.012

    Figure Lengend Snippet: Atomic Model of the MDA5-dsRNA Filament (A) Domain structure of mouse MDA5. CARD, caspase recruitment domain; CTD, C-terminal domain; Hel1 and Hel2, first and second RecA-like helicase domains; Hel2i, Hel2 insert domain; P, pincer domain. The same color code and domain abbreviations are used in subsequent panels and in Figures 1 , 7A, and 7 D. (B) Overview of the refined atomic model of the MDA5-dsRNA filament. Two adjacent MDA5 subunits and 28 bp of dsRNA are shown from the Twist74 structure. RNA is in magenta. The bound AMPPNP molecules are shown in sphere representation. The two filament-forming interfaces are boxed. (C and D) Close-up views of filament interface II (C) and interface I (D). The top panels show side chains forming key contacts, with hydrogen bonds shown as yellow dashed lines. In the middle panels the lower protomer in (B) is shown in surface representation colored by hydrophobicity from gray to green, with green being the most hydrophobic. In the lower panels, the upper protomer in (B) is shown in surface representation colored by hydrophobicity. The orientation of the view relative to (B) is indicated for each panel. See also Figure S3 and Videos S1 , S2 , S3 , S4 , and S5 .

    Article Snippet: Mouse MDA5 protein (WT or ATPase-defective mutant) was titrated from 0 to 40 μM into a solution containing 10 μM Mant-AMPPNP and poly(I:C) RNA at a 1:3 molar ratio of MDA5 to RNA binding sites, assuming 15 bp per binding site.

    Techniques:

    Cryo-EM Image Reconstruction of MDA5-dsRNA Filaments with Helical Symmetry Averaging (A) Representative cryo-EM micrograph of MDA5-dsRNA filaments. (B) Cryo-EM micrograph shown in (A) with circles drawn around the boxed filament segments that were used in the helical reconstructions. The circles are colored according to the 3D class that they contributed to. Segments that contributed to the Twist74, Twist87, and Twist91 structures are in red, green, and blue, respectively. (C) Histogram showing the distributions of filament segments as a function of helical twist for the ATP, ADP-AlF 4 , 1-mM AMPPNP, and nucleotide-free datasets. The distributions shown are from 3D classification performed with ten classes per dataset. Error bars represent SEM between replicate 3D classification calculations; n = 3. (D) 3D density map of the Twist74 MDA5-dsRNA filament at 3.68 Å overall resolution. The components are colored as follows: Hel1, green; Hel2, cyan; Hel2i, yellow; pincer domain, red; CTD, orange; and RNA, magenta. (E) The dsRNA density in the Twist74 filament (blue mesh) is shown with the fitted atomic model (magenta and pink). See also Figures S1 and S2 .

    Journal: Molecular Cell

    Article Title: Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis

    doi: 10.1016/j.molcel.2018.10.012

    Figure Lengend Snippet: Cryo-EM Image Reconstruction of MDA5-dsRNA Filaments with Helical Symmetry Averaging (A) Representative cryo-EM micrograph of MDA5-dsRNA filaments. (B) Cryo-EM micrograph shown in (A) with circles drawn around the boxed filament segments that were used in the helical reconstructions. The circles are colored according to the 3D class that they contributed to. Segments that contributed to the Twist74, Twist87, and Twist91 structures are in red, green, and blue, respectively. (C) Histogram showing the distributions of filament segments as a function of helical twist for the ATP, ADP-AlF 4 , 1-mM AMPPNP, and nucleotide-free datasets. The distributions shown are from 3D classification performed with ten classes per dataset. Error bars represent SEM between replicate 3D classification calculations; n = 3. (D) 3D density map of the Twist74 MDA5-dsRNA filament at 3.68 Å overall resolution. The components are colored as follows: Hel1, green; Hel2, cyan; Hel2i, yellow; pincer domain, red; CTD, orange; and RNA, magenta. (E) The dsRNA density in the Twist74 filament (blue mesh) is shown with the fitted atomic model (magenta and pink). See also Figures S1 and S2 .

    Article Snippet: Mouse MDA5 protein (WT or ATPase-defective mutant) was titrated from 0 to 40 μM into a solution containing 10 μM Mant-AMPPNP and poly(I:C) RNA at a 1:3 molar ratio of MDA5 to RNA binding sites, assuming 15 bp per binding site.

    Techniques:

    Comparison of the Closed ADP-AlF 4 -Bound Structure with the Semi-open Structures and Schematic Model of the ATPase Cycle and Proofreading Mechanism of MDA5 For a Figure360 author presentation of Figure 7, see https://doi.org/10.1016/j.molcel.2018.10.012 . (A) Close-up view of the nucleotide-binding site and Hel1-Hel2 domain interface. The Twist74 AMPPNP-bound structure (blue) was superimposed on the ADP-AlF 4 -bound structure (colored by domain as in Figure 2 ) using the Hel1 domain as the reference. Nucleotide-binding motifs Va and VI are labeled. Only the ADP-AlF 4 nucleotide is shown for clarity. (B) Close-up view of the Hel2-loop and its interactions with the dsRNA. The Twist74 (blue) and Twist87 (pink) AMPPNP-bound structures are superimposed onto the ADP-AlF 4 -bound structure (green) using Hel1 as the reference. (C) Overview of Twist74 (blue) superimposed on the ADP-AlF 4 -bound structure (green) using Hel1 as the reference. (D) Model of the ATPase cycle and proofreading mechanism. Only two filament protomers are shown for clarity. The low-twist (71°–81°) structures correspond to the ATP-bound catalytic ground state, the intermediate-twist (81°–91°) ADP-AlF 4 -bound structure is the transition state, and the intermediate- and high-twist (91°–96°) states represent nucleotide-free states. The four panels relate to the panels in Figures 3 C–3F. See also Videos S1 , S2 , S3 , S4 , and S5 . Figure360: An Author Presentation of Figure 7

    Journal: Molecular Cell

    Article Title: Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis

    doi: 10.1016/j.molcel.2018.10.012

    Figure Lengend Snippet: Comparison of the Closed ADP-AlF 4 -Bound Structure with the Semi-open Structures and Schematic Model of the ATPase Cycle and Proofreading Mechanism of MDA5 For a Figure360 author presentation of Figure 7, see https://doi.org/10.1016/j.molcel.2018.10.012 . (A) Close-up view of the nucleotide-binding site and Hel1-Hel2 domain interface. The Twist74 AMPPNP-bound structure (blue) was superimposed on the ADP-AlF 4 -bound structure (colored by domain as in Figure 2 ) using the Hel1 domain as the reference. Nucleotide-binding motifs Va and VI are labeled. Only the ADP-AlF 4 nucleotide is shown for clarity. (B) Close-up view of the Hel2-loop and its interactions with the dsRNA. The Twist74 (blue) and Twist87 (pink) AMPPNP-bound structures are superimposed onto the ADP-AlF 4 -bound structure (green) using Hel1 as the reference. (C) Overview of Twist74 (blue) superimposed on the ADP-AlF 4 -bound structure (green) using Hel1 as the reference. (D) Model of the ATPase cycle and proofreading mechanism. Only two filament protomers are shown for clarity. The low-twist (71°–81°) structures correspond to the ATP-bound catalytic ground state, the intermediate-twist (81°–91°) ADP-AlF 4 -bound structure is the transition state, and the intermediate- and high-twist (91°–96°) states represent nucleotide-free states. The four panels relate to the panels in Figures 3 C–3F. See also Videos S1 , S2 , S3 , S4 , and S5 . Figure360: An Author Presentation of Figure 7

    Article Snippet: 10 μM Mant-AMPPNP was selected for the assay as it was the minimum concentration required for detection of fluorescent signal relative to a blank containing 10 μM (1.14 g l−1 ) MDA5 and 0.303 g l−1 poly(I:C) RNA but no Mant-AMPPNP.

    Techniques: Binding Assay, Labeling

    Interface Mutations that Impair Signaling Also Impair Filament Formation (A) Representative electron micrographs of MDA5 filament interface mutants in the presence of 1 kb dsRNA, 1 mM AMPPNP, and 5 mM MgCl 2 . Scale bars, 100 nm. Residue numbers refer to mouse MDA5. (B) Table summarizing the filament formation activity, filament length, cell-signaling activity, and ATPase activity of selected MDA5 mutants. ATPase activities were calculated from the initial slopes of the curves in Figure 5 D and is expressed as moles of released phosphate per mole of MDA5 per second (M Pi M MDA5 −1 s −1 ). Residue numbers refer to mouse MDA5. For mutants with different residue numbers in human MDA5, the corresponding mutation is shown in human residue numbers at the bottom. n.d., not determined. See also Figures S5 and S7 .

    Journal: Molecular Cell

    Article Title: Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis

    doi: 10.1016/j.molcel.2018.10.012

    Figure Lengend Snippet: Interface Mutations that Impair Signaling Also Impair Filament Formation (A) Representative electron micrographs of MDA5 filament interface mutants in the presence of 1 kb dsRNA, 1 mM AMPPNP, and 5 mM MgCl 2 . Scale bars, 100 nm. Residue numbers refer to mouse MDA5. (B) Table summarizing the filament formation activity, filament length, cell-signaling activity, and ATPase activity of selected MDA5 mutants. ATPase activities were calculated from the initial slopes of the curves in Figure 5 D and is expressed as moles of released phosphate per mole of MDA5 per second (M Pi M MDA5 −1 s −1 ). Residue numbers refer to mouse MDA5. For mutants with different residue numbers in human MDA5, the corresponding mutation is shown in human residue numbers at the bottom. n.d., not determined. See also Figures S5 and S7 .

    Article Snippet: 10 μM Mant-AMPPNP was selected for the assay as it was the minimum concentration required for detection of fluorescent signal relative to a blank containing 10 μM (1.14 g l−1 ) MDA5 and 0.303 g l−1 poly(I:C) RNA but no Mant-AMPPNP.

    Techniques: Activity Assay, Mutagenesis