reference strains staphylococcus aureus atcc 29213 Search Results


29213 in dmem  (Biochrom)
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Biochrom 29213 in dmem
29213 In Dmem, supplied by Biochrom, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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rnap ttc emd 29213 cryo em maps  (Thermo Fisher)
86
Thermo Fisher rnap ttc emd 29213 cryo em maps
(A) Left, <t>cryo-EM</t> structure of <t>RNAP</t> harboring a terminal mismatch ( RNAP Free ). Right, a cross-section of the EM reconstruction is shown fitted with the coordinate model. (B) Close-up view of the RNAP Free active site. RNAP Free is in a backtracked conformation, in which ten RNA bases appear hybridized with the tDNA up to the i+1 position (threshold values at δ = 0.1–0.07) and the backtracked ribonucleotide is observed flipped out of the hybrid helix path (threshold values at δ = 0.05–0.04). (C) Combined cryo-EM structure of the TTC. (D) The RNAP-ribosome interaction surface. Top: cartoon views of RNAP and the ribosome 30S subunit in the TTC structure, in which potential intermolecular interactions are outlined by dashed boxes, with close-up views at the bottom. (E) Left, inner view of the TTC model showing the mRNA path from the RNAP TTC active site to the P-site tRNA.. (F) Close-up view of the RNAP TTC active site. RNAP TTC is in a post-translocated state, in which nine RNA bases appear hybridized with the DNA up to the i position. (G) Swiveling of RNAP Free versus RNAP TTC . Coordinates of both structures were aligned relative to the core module of RNAP (gray ribbon) and it was observed that the swivel module of RNAP TTC was rotated −2.3° towards an anti-swiveled direction relative to that of RNAP Free . Right, close-up views of the β ′ -clamp, downstream DNA duplex and, β ′ -SI3 regions. (H) Multibody analysis of the β ′ SI3 domain ‘inward’ dynamics, in both the RNAP Free (top) and RNAP TTC (bottom). See also , , and .
Rnap Ttc Emd 29213 Cryo Em Maps, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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staphylococcus aureus  (Becton Dickinson)
86
Becton Dickinson staphylococcus aureus
(A) Left, <t>cryo-EM</t> structure of <t>RNAP</t> harboring a terminal mismatch ( RNAP Free ). Right, a cross-section of the EM reconstruction is shown fitted with the coordinate model. (B) Close-up view of the RNAP Free active site. RNAP Free is in a backtracked conformation, in which ten RNA bases appear hybridized with the tDNA up to the i+1 position (threshold values at δ = 0.1–0.07) and the backtracked ribonucleotide is observed flipped out of the hybrid helix path (threshold values at δ = 0.05–0.04). (C) Combined cryo-EM structure of the TTC. (D) The RNAP-ribosome interaction surface. Top: cartoon views of RNAP and the ribosome 30S subunit in the TTC structure, in which potential intermolecular interactions are outlined by dashed boxes, with close-up views at the bottom. (E) Left, inner view of the TTC model showing the mRNA path from the RNAP TTC active site to the P-site tRNA.. (F) Close-up view of the RNAP TTC active site. RNAP TTC is in a post-translocated state, in which nine RNA bases appear hybridized with the DNA up to the i position. (G) Swiveling of RNAP Free versus RNAP TTC . Coordinates of both structures were aligned relative to the core module of RNAP (gray ribbon) and it was observed that the swivel module of RNAP TTC was rotated −2.3° towards an anti-swiveled direction relative to that of RNAP Free . Right, close-up views of the β ′ -clamp, downstream DNA duplex and, β ′ -SI3 regions. (H) Multibody analysis of the β ′ SI3 domain ‘inward’ dynamics, in both the RNAP Free (top) and RNAP TTC (bottom). See also , , and .
Staphylococcus Aureus, supplied by Becton Dickinson, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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tsaps  (Becton Dickinson)
86
Becton Dickinson tsaps
(A) Left, <t>cryo-EM</t> structure of <t>RNAP</t> harboring a terminal mismatch ( RNAP Free ). Right, a cross-section of the EM reconstruction is shown fitted with the coordinate model. (B) Close-up view of the RNAP Free active site. RNAP Free is in a backtracked conformation, in which ten RNA bases appear hybridized with the tDNA up to the i+1 position (threshold values at δ = 0.1–0.07) and the backtracked ribonucleotide is observed flipped out of the hybrid helix path (threshold values at δ = 0.05–0.04). (C) Combined cryo-EM structure of the TTC. (D) The RNAP-ribosome interaction surface. Top: cartoon views of RNAP and the ribosome 30S subunit in the TTC structure, in which potential intermolecular interactions are outlined by dashed boxes, with close-up views at the bottom. (E) Left, inner view of the TTC model showing the mRNA path from the RNAP TTC active site to the P-site tRNA.. (F) Close-up view of the RNAP TTC active site. RNAP TTC is in a post-translocated state, in which nine RNA bases appear hybridized with the DNA up to the i position. (G) Swiveling of RNAP Free versus RNAP TTC . Coordinates of both structures were aligned relative to the core module of RNAP (gray ribbon) and it was observed that the swivel module of RNAP TTC was rotated −2.3° towards an anti-swiveled direction relative to that of RNAP Free . Right, close-up views of the β ′ -clamp, downstream DNA duplex and, β ′ -SI3 regions. (H) Multibody analysis of the β ′ SI3 domain ‘inward’ dynamics, in both the RNAP Free (top) and RNAP TTC (bottom). See also , , and .
Tsaps, supplied by Becton Dickinson, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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mhaps  (Becton Dickinson)
86
Becton Dickinson mhaps
(A) Left, <t>cryo-EM</t> structure of <t>RNAP</t> harboring a terminal mismatch ( RNAP Free ). Right, a cross-section of the EM reconstruction is shown fitted with the coordinate model. (B) Close-up view of the RNAP Free active site. RNAP Free is in a backtracked conformation, in which ten RNA bases appear hybridized with the tDNA up to the i+1 position (threshold values at δ = 0.1–0.07) and the backtracked ribonucleotide is observed flipped out of the hybrid helix path (threshold values at δ = 0.05–0.04). (C) Combined cryo-EM structure of the TTC. (D) The RNAP-ribosome interaction surface. Top: cartoon views of RNAP and the ribosome 30S subunit in the TTC structure, in which potential intermolecular interactions are outlined by dashed boxes, with close-up views at the bottom. (E) Left, inner view of the TTC model showing the mRNA path from the RNAP TTC active site to the P-site tRNA.. (F) Close-up view of the RNAP TTC active site. RNAP TTC is in a post-translocated state, in which nine RNA bases appear hybridized with the DNA up to the i position. (G) Swiveling of RNAP Free versus RNAP TTC . Coordinates of both structures were aligned relative to the core module of RNAP (gray ribbon) and it was observed that the swivel module of RNAP TTC was rotated −2.3° towards an anti-swiveled direction relative to that of RNAP Free . Right, close-up views of the β ′ -clamp, downstream DNA duplex and, β ′ -SI3 regions. (H) Multibody analysis of the β ′ SI3 domain ‘inward’ dynamics, in both the RNAP Free (top) and RNAP TTC (bottom). See also , , and .
Mhaps, supplied by Becton Dickinson, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 86 stars, based on 1 article reviews
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Image Search Results


(A) Left, cryo-EM structure of RNAP harboring a terminal mismatch ( RNAP Free ). Right, a cross-section of the EM reconstruction is shown fitted with the coordinate model. (B) Close-up view of the RNAP Free active site. RNAP Free is in a backtracked conformation, in which ten RNA bases appear hybridized with the tDNA up to the i+1 position (threshold values at δ = 0.1–0.07) and the backtracked ribonucleotide is observed flipped out of the hybrid helix path (threshold values at δ = 0.05–0.04). (C) Combined cryo-EM structure of the TTC. (D) The RNAP-ribosome interaction surface. Top: cartoon views of RNAP and the ribosome 30S subunit in the TTC structure, in which potential intermolecular interactions are outlined by dashed boxes, with close-up views at the bottom. (E) Left, inner view of the TTC model showing the mRNA path from the RNAP TTC active site to the P-site tRNA.. (F) Close-up view of the RNAP TTC active site. RNAP TTC is in a post-translocated state, in which nine RNA bases appear hybridized with the DNA up to the i position. (G) Swiveling of RNAP Free versus RNAP TTC . Coordinates of both structures were aligned relative to the core module of RNAP (gray ribbon) and it was observed that the swivel module of RNAP TTC was rotated −2.3° towards an anti-swiveled direction relative to that of RNAP Free . Right, close-up views of the β ′ -clamp, downstream DNA duplex and, β ′ -SI3 regions. (H) Multibody analysis of the β ′ SI3 domain ‘inward’ dynamics, in both the RNAP Free (top) and RNAP TTC (bottom). See also , , and .

Journal: Cell

Article Title: A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery

doi: 10.1016/j.cell.2023.02.008

Figure Lengend Snippet: (A) Left, cryo-EM structure of RNAP harboring a terminal mismatch ( RNAP Free ). Right, a cross-section of the EM reconstruction is shown fitted with the coordinate model. (B) Close-up view of the RNAP Free active site. RNAP Free is in a backtracked conformation, in which ten RNA bases appear hybridized with the tDNA up to the i+1 position (threshold values at δ = 0.1–0.07) and the backtracked ribonucleotide is observed flipped out of the hybrid helix path (threshold values at δ = 0.05–0.04). (C) Combined cryo-EM structure of the TTC. (D) The RNAP-ribosome interaction surface. Top: cartoon views of RNAP and the ribosome 30S subunit in the TTC structure, in which potential intermolecular interactions are outlined by dashed boxes, with close-up views at the bottom. (E) Left, inner view of the TTC model showing the mRNA path from the RNAP TTC active site to the P-site tRNA.. (F) Close-up view of the RNAP TTC active site. RNAP TTC is in a post-translocated state, in which nine RNA bases appear hybridized with the DNA up to the i position. (G) Swiveling of RNAP Free versus RNAP TTC . Coordinates of both structures were aligned relative to the core module of RNAP (gray ribbon) and it was observed that the swivel module of RNAP TTC was rotated −2.3° towards an anti-swiveled direction relative to that of RNAP Free . Right, close-up views of the β ′ -clamp, downstream DNA duplex and, β ′ -SI3 regions. (H) Multibody analysis of the β ′ SI3 domain ‘inward’ dynamics, in both the RNAP Free (top) and RNAP TTC (bottom). See also , , and .

Article Snippet: The resulting transformation matricies were then used to align the corresponding RNAP Free (EMD-29212) to the RNAP TTC (EMD-29213) cryo-EM maps using the coord_transform_to_star program ( https://github.com/dominikaherbst/cryo-em_scripts ), and used the volume resample tool in ChimeraX to generate the aligned version of the RNAP Free cryo-EM map.

Techniques: Cryo-EM Sample Prep