Structured Review

Biotechnology Information protein data bank pdb
In silico , Red, UbcH7; green, cbl; yellow, <t>RAG1;</t> magenta spheres, cbl zinc ions; grey spheres, RAG1 zinc ions. Protein Data Bank <t>(PDB)</t> ID for the cbl–ubcH7 co-structure is 1fbv, PDB ID for RAG1 RING is 1rmd.
Protein Data Bank Pdb, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 91/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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91/100 stars

Images

1) Product Images from "Correlation between recombinase activating gene 1 ubiquitin ligase activity and V(D)J recombination"

Article Title: Correlation between recombinase activating gene 1 ubiquitin ligase activity and V(D)J recombination

Journal: Immunology

doi: 10.1111/j.1365-2567.2009.03101.x

In silico , Red, UbcH7; green, cbl; yellow, RAG1; magenta spheres, cbl zinc ions; grey spheres, RAG1 zinc ions. Protein Data Bank (PDB) ID for the cbl–ubcH7 co-structure is 1fbv, PDB ID for RAG1 RING is 1rmd.
Figure Legend Snippet: In silico , Red, UbcH7; green, cbl; yellow, RAG1; magenta spheres, cbl zinc ions; grey spheres, RAG1 zinc ions. Protein Data Bank (PDB) ID for the cbl–ubcH7 co-structure is 1fbv, PDB ID for RAG1 RING is 1rmd.

Techniques Used: In Silico

2) Product Images from "Natural Products as New Treatment Options for Trichomoniasis: A Molecular Docking Investigation"

Article Title: Natural Products as New Treatment Options for Trichomoniasis: A Molecular Docking Investigation

Journal: Scientia Pharmaceutica

doi: 10.3390/scipharm85010005

Overlay of the protein structures of human cathepsin V, PDB 1FH0 [ 26 ] (red ribbon), and the homology model of Trichomonas vaginalis cathepsin L-like protein, TvCPCAC1 (blue ribbon). The co-crystallized ligand is shown as a wireframe structure.
Figure Legend Snippet: Overlay of the protein structures of human cathepsin V, PDB 1FH0 [ 26 ] (red ribbon), and the homology model of Trichomonas vaginalis cathepsin L-like protein, TvCPCAC1 (blue ribbon). The co-crystallized ligand is shown as a wireframe structure.

Techniques Used:

Overlay of the protein structures of Brucella melitensis TxR, PDB 4JNQ [ 24 ] (red ribbon), and the homology model of Trichomonas vaginalis TxR (blue ribbon). The co-crystallized ligand is shown as a wireframe structure.
Figure Legend Snippet: Overlay of the protein structures of Brucella melitensis TxR, PDB 4JNQ [ 24 ] (red ribbon), and the homology model of Trichomonas vaginalis TxR (blue ribbon). The co-crystallized ligand is shown as a wireframe structure.

Techniques Used:

Ramachandran plots of cathepsin V-like protein structures: ( a ) human cathepsin V (HsCatV, PDB 1FH0 [ 26 ]); ( b ) homology model of Trichomonas vaginalis cathepsin L-like protein, TvCPCAC1; ( c ) binding site of HsCatV; ( d ) binding site of TvCPCAC1.
Figure Legend Snippet: Ramachandran plots of cathepsin V-like protein structures: ( a ) human cathepsin V (HsCatV, PDB 1FH0 [ 26 ]); ( b ) homology model of Trichomonas vaginalis cathepsin L-like protein, TvCPCAC1; ( c ) binding site of HsCatV; ( d ) binding site of TvCPCAC1.

Techniques Used: Binding Assay

Ramachandran plots of cathepsin K-like protein structures: ( a ) rabbit ( Oryctolagus cuniculus ) cathepsin K (OcCatK, PDB 2F7D [ 25 ]); ( b ) homology model of Trichomonas vaginalis papain-like protein, TvCP2; ( c ) binding site of OcCatK; ( d ) binding site of TvCP2.
Figure Legend Snippet: Ramachandran plots of cathepsin K-like protein structures: ( a ) rabbit ( Oryctolagus cuniculus ) cathepsin K (OcCatK, PDB 2F7D [ 25 ]); ( b ) homology model of Trichomonas vaginalis papain-like protein, TvCP2; ( c ) binding site of OcCatK; ( d ) binding site of TvCP2.

Techniques Used: Binding Assay

Lowest-energy re-docked poses of co-crystallized ligands: ( a ) Trichomonas vaginalis methionine gamma-lyase (TvMGL, PDB 1E5F [ 27 ]) showing the co-crystallized ligand, pyridoxal-5′-phosphate (green), and the re-docked ligand (magenta); ( b ) T. vaginalis purine nucleoside phosphorylase (TvPNP, PDB 1Z36 [ 28 ]) showing the co-crystallized ligand, (1 S )-1-(7-amino-1 H -pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro- d -ribitol (green), and the re-docked ligand (red); ( c ) human cathepsin K (HsCatK, PDB 1U9V [ 38 ]) showing the co-crystallized ligand, 6-(cyclohexylamino)-9-[2-(4-methylpiperazin-1-yl)-ethyl]-9 H -purine-2-carbonitrile (green), and the re-docked ligand (blue); and ( d ) human cathepsin L (HsCatL, PDB 3HWN [ 39 ]) showing the co-crystallized ligand, N -α-[(3- t -Butyl-1-methyl-1 H -pyrazol-5-yl)carbonyl]- N -[(2 E )-2-iminoethyl]-3-{5-[( Z )-iminomethyl]-1,3,4-oxadiazol-2-yl}- l -phenylalaninamide (green), and the re-docked ligand (aqua).
Figure Legend Snippet: Lowest-energy re-docked poses of co-crystallized ligands: ( a ) Trichomonas vaginalis methionine gamma-lyase (TvMGL, PDB 1E5F [ 27 ]) showing the co-crystallized ligand, pyridoxal-5′-phosphate (green), and the re-docked ligand (magenta); ( b ) T. vaginalis purine nucleoside phosphorylase (TvPNP, PDB 1Z36 [ 28 ]) showing the co-crystallized ligand, (1 S )-1-(7-amino-1 H -pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro- d -ribitol (green), and the re-docked ligand (red); ( c ) human cathepsin K (HsCatK, PDB 1U9V [ 38 ]) showing the co-crystallized ligand, 6-(cyclohexylamino)-9-[2-(4-methylpiperazin-1-yl)-ethyl]-9 H -purine-2-carbonitrile (green), and the re-docked ligand (blue); and ( d ) human cathepsin L (HsCatL, PDB 3HWN [ 39 ]) showing the co-crystallized ligand, N -α-[(3- t -Butyl-1-methyl-1 H -pyrazol-5-yl)carbonyl]- N -[(2 E )-2-iminoethyl]-3-{5-[( Z )-iminomethyl]-1,3,4-oxadiazol-2-yl}- l -phenylalaninamide (green), and the re-docked ligand (aqua).

Techniques Used:

Overlay of the protein structures of rabbit ( Oryctolagus cuniculus ) cathepsin K, PDB 2F7D [ 25 ] (red ribbon), and the homology model of Trichomonas vaginalis papain-like protein, TvCP2 (blue ribbon). The co-crystallized ligand is shown as a wireframe structure.
Figure Legend Snippet: Overlay of the protein structures of rabbit ( Oryctolagus cuniculus ) cathepsin K, PDB 2F7D [ 25 ] (red ribbon), and the homology model of Trichomonas vaginalis papain-like protein, TvCP2 (blue ribbon). The co-crystallized ligand is shown as a wireframe structure.

Techniques Used:

Related Articles

Sequencing:

Article Title: Structural and functional analyses of the N-terminal domain of the A subunit of a Bacillus megaterium spore germinant receptor
Article Snippet: .. Although primary amino acid sequence analysis failed to identify any known protein motif in GerK3 ANTD , a structure homology search of the Protein Data Bank (PDB) using the National Center for Biotechnology Information’s (NCBI) Vector Alignment Search Tool (VAST+) ( ) revealed that both the N1 and N2 domains of GerK3 ANTD share a common fold with bacterial periplasmic-binding proteins (PeBPs) (Pfam database identification numbers CL0177 and CL0144). ..

Article Title: Illumination of PRRSV Cytotoxic T Lymphocyte Epitopes by the Three-Dimensional Structure and Peptidome of Swine Lymphocyte Antigen Class I (SLA-I)
Article Snippet: .. Data Availability Statement The coordinates and structural characteristics of pSLA-1* 1502 have been deposited in the Protein Data Bank under accession number 5YLX ; the sequence of SLA-1* 1502 is available at the National Center for Biotechnology Information (NCBI) database under accession number HQ909439 . ..

Genomic Sequencing:

Article Title: Genomics and Privacy: Implications of the New Reality of Closed Data for the Field
Article Snippet: .. Much open data has been available to the bioinformatics community from a variety of databases, including the Protein Data Bank (PDB), a repository for macromolecular structures (established 1971), and the National Center for Biotechnology Information (NCBI), which houses genomic sequences and other biotechnology-related information (1988) . ..

Construct:

Article Title: Natural Products as New Treatment Options for Trichomoniasis: A Molecular Docking Investigation
Article Snippet: .. Homology Modeling Homology models for each of the Trichomonas proteins that are not currently available from the Protein Data Bank (PDB) were constructed from crystal structure templates found in the Protein Data Bank using FASTA sequences downloaded from the National Center for Biotechnology Information’s (NCBI) GenBank. .. Sequences with high sequence similarity in the PDB were identified with NCBI’s BLAST utility using the BLOSUM80 scoring matrix (BLOcks SUbstitution Matrix).

Plasmid Preparation:

Article Title: Structural and functional analyses of the N-terminal domain of the A subunit of a Bacillus megaterium spore germinant receptor
Article Snippet: .. Although primary amino acid sequence analysis failed to identify any known protein motif in GerK3 ANTD , a structure homology search of the Protein Data Bank (PDB) using the National Center for Biotechnology Information’s (NCBI) Vector Alignment Search Tool (VAST+) ( ) revealed that both the N1 and N2 domains of GerK3 ANTD share a common fold with bacterial periplasmic-binding proteins (PeBPs) (Pfam database identification numbers CL0177 and CL0144). ..

In Silico:

Article Title: Correlation between recombinase activating gene 1 ubiquitin ligase activity and V(D)J recombination
Article Snippet: .. The interface between CDC34 and RAG1 was predicted based on in silico alignment of the RAG1 RING and cbl-UbcH7 crystal structures obtained using the Protein Data Bank (PDB) co-ordinates available from the National Center for Biotechnology Information (NCBI) structural database., Initial manual alignments allowed us to designate 32 residue pairs in equivalent positions in the two structures, and these were aligned using the least square fit protocol of the align program (Shareware). ..

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    Biotechnology Information protein data bank pdb
    In silico , Red, UbcH7; green, cbl; yellow, <t>RAG1;</t> magenta spheres, cbl zinc ions; grey spheres, RAG1 zinc ions. Protein Data Bank <t>(PDB)</t> ID for the cbl–ubcH7 co-structure is 1fbv, PDB ID for RAG1 RING is 1rmd.
    Protein Data Bank Pdb, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 91/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/protein data bank pdb/product/Biotechnology Information
    Average 91 stars, based on 10 article reviews
    Price from $9.99 to $1999.99
    protein data bank pdb - by Bioz Stars, 2020-09
    91/100 stars
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    85
    Biotechnology Information wt tlr2 structure
    Expression levels and signaling capacities of WT and R753Q <t>YFP-TLR2</t> species. A–D , HEK293 cells were transiently ( A , C , and D ) or stably ( B ) transfected with expression vectors encoding WT or R753Q YFP-TLR2 variants. A , after recovery for 48 h,
    Wt Tlr2 Structure, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 85 stars, based on 1 article reviews
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    Image Search Results


    In silico , Red, UbcH7; green, cbl; yellow, RAG1; magenta spheres, cbl zinc ions; grey spheres, RAG1 zinc ions. Protein Data Bank (PDB) ID for the cbl–ubcH7 co-structure is 1fbv, PDB ID for RAG1 RING is 1rmd.

    Journal: Immunology

    Article Title: Correlation between recombinase activating gene 1 ubiquitin ligase activity and V(D)J recombination

    doi: 10.1111/j.1365-2567.2009.03101.x

    Figure Lengend Snippet: In silico , Red, UbcH7; green, cbl; yellow, RAG1; magenta spheres, cbl zinc ions; grey spheres, RAG1 zinc ions. Protein Data Bank (PDB) ID for the cbl–ubcH7 co-structure is 1fbv, PDB ID for RAG1 RING is 1rmd.

    Article Snippet: The interface between CDC34 and RAG1 was predicted based on in silico alignment of the RAG1 RING and cbl-UbcH7 crystal structures obtained using the Protein Data Bank (PDB) co-ordinates available from the National Center for Biotechnology Information (NCBI) structural database., Initial manual alignments allowed us to designate 32 residue pairs in equivalent positions in the two structures, and these were aligned using the least square fit protocol of the align program (Shareware).

    Techniques: In Silico

    Overlay of the protein structures of human cathepsin V, PDB 1FH0 [ 26 ] (red ribbon), and the homology model of Trichomonas vaginalis cathepsin L-like protein, TvCPCAC1 (blue ribbon). The co-crystallized ligand is shown as a wireframe structure.

    Journal: Scientia Pharmaceutica

    Article Title: Natural Products as New Treatment Options for Trichomoniasis: A Molecular Docking Investigation

    doi: 10.3390/scipharm85010005

    Figure Lengend Snippet: Overlay of the protein structures of human cathepsin V, PDB 1FH0 [ 26 ] (red ribbon), and the homology model of Trichomonas vaginalis cathepsin L-like protein, TvCPCAC1 (blue ribbon). The co-crystallized ligand is shown as a wireframe structure.

    Article Snippet: Homology Modeling Homology models for each of the Trichomonas proteins that are not currently available from the Protein Data Bank (PDB) were constructed from crystal structure templates found in the Protein Data Bank using FASTA sequences downloaded from the National Center for Biotechnology Information’s (NCBI) GenBank.

    Techniques:

    Overlay of the protein structures of Brucella melitensis TxR, PDB 4JNQ [ 24 ] (red ribbon), and the homology model of Trichomonas vaginalis TxR (blue ribbon). The co-crystallized ligand is shown as a wireframe structure.

    Journal: Scientia Pharmaceutica

    Article Title: Natural Products as New Treatment Options for Trichomoniasis: A Molecular Docking Investigation

    doi: 10.3390/scipharm85010005

    Figure Lengend Snippet: Overlay of the protein structures of Brucella melitensis TxR, PDB 4JNQ [ 24 ] (red ribbon), and the homology model of Trichomonas vaginalis TxR (blue ribbon). The co-crystallized ligand is shown as a wireframe structure.

    Article Snippet: Homology Modeling Homology models for each of the Trichomonas proteins that are not currently available from the Protein Data Bank (PDB) were constructed from crystal structure templates found in the Protein Data Bank using FASTA sequences downloaded from the National Center for Biotechnology Information’s (NCBI) GenBank.

    Techniques:

    Ramachandran plots of cathepsin V-like protein structures: ( a ) human cathepsin V (HsCatV, PDB 1FH0 [ 26 ]); ( b ) homology model of Trichomonas vaginalis cathepsin L-like protein, TvCPCAC1; ( c ) binding site of HsCatV; ( d ) binding site of TvCPCAC1.

    Journal: Scientia Pharmaceutica

    Article Title: Natural Products as New Treatment Options for Trichomoniasis: A Molecular Docking Investigation

    doi: 10.3390/scipharm85010005

    Figure Lengend Snippet: Ramachandran plots of cathepsin V-like protein structures: ( a ) human cathepsin V (HsCatV, PDB 1FH0 [ 26 ]); ( b ) homology model of Trichomonas vaginalis cathepsin L-like protein, TvCPCAC1; ( c ) binding site of HsCatV; ( d ) binding site of TvCPCAC1.

    Article Snippet: Homology Modeling Homology models for each of the Trichomonas proteins that are not currently available from the Protein Data Bank (PDB) were constructed from crystal structure templates found in the Protein Data Bank using FASTA sequences downloaded from the National Center for Biotechnology Information’s (NCBI) GenBank.

    Techniques: Binding Assay

    Ramachandran plots of cathepsin K-like protein structures: ( a ) rabbit ( Oryctolagus cuniculus ) cathepsin K (OcCatK, PDB 2F7D [ 25 ]); ( b ) homology model of Trichomonas vaginalis papain-like protein, TvCP2; ( c ) binding site of OcCatK; ( d ) binding site of TvCP2.

    Journal: Scientia Pharmaceutica

    Article Title: Natural Products as New Treatment Options for Trichomoniasis: A Molecular Docking Investigation

    doi: 10.3390/scipharm85010005

    Figure Lengend Snippet: Ramachandran plots of cathepsin K-like protein structures: ( a ) rabbit ( Oryctolagus cuniculus ) cathepsin K (OcCatK, PDB 2F7D [ 25 ]); ( b ) homology model of Trichomonas vaginalis papain-like protein, TvCP2; ( c ) binding site of OcCatK; ( d ) binding site of TvCP2.

    Article Snippet: Homology Modeling Homology models for each of the Trichomonas proteins that are not currently available from the Protein Data Bank (PDB) were constructed from crystal structure templates found in the Protein Data Bank using FASTA sequences downloaded from the National Center for Biotechnology Information’s (NCBI) GenBank.

    Techniques: Binding Assay

    Lowest-energy re-docked poses of co-crystallized ligands: ( a ) Trichomonas vaginalis methionine gamma-lyase (TvMGL, PDB 1E5F [ 27 ]) showing the co-crystallized ligand, pyridoxal-5′-phosphate (green), and the re-docked ligand (magenta); ( b ) T. vaginalis purine nucleoside phosphorylase (TvPNP, PDB 1Z36 [ 28 ]) showing the co-crystallized ligand, (1 S )-1-(7-amino-1 H -pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro- d -ribitol (green), and the re-docked ligand (red); ( c ) human cathepsin K (HsCatK, PDB 1U9V [ 38 ]) showing the co-crystallized ligand, 6-(cyclohexylamino)-9-[2-(4-methylpiperazin-1-yl)-ethyl]-9 H -purine-2-carbonitrile (green), and the re-docked ligand (blue); and ( d ) human cathepsin L (HsCatL, PDB 3HWN [ 39 ]) showing the co-crystallized ligand, N -α-[(3- t -Butyl-1-methyl-1 H -pyrazol-5-yl)carbonyl]- N -[(2 E )-2-iminoethyl]-3-{5-[( Z )-iminomethyl]-1,3,4-oxadiazol-2-yl}- l -phenylalaninamide (green), and the re-docked ligand (aqua).

    Journal: Scientia Pharmaceutica

    Article Title: Natural Products as New Treatment Options for Trichomoniasis: A Molecular Docking Investigation

    doi: 10.3390/scipharm85010005

    Figure Lengend Snippet: Lowest-energy re-docked poses of co-crystallized ligands: ( a ) Trichomonas vaginalis methionine gamma-lyase (TvMGL, PDB 1E5F [ 27 ]) showing the co-crystallized ligand, pyridoxal-5′-phosphate (green), and the re-docked ligand (magenta); ( b ) T. vaginalis purine nucleoside phosphorylase (TvPNP, PDB 1Z36 [ 28 ]) showing the co-crystallized ligand, (1 S )-1-(7-amino-1 H -pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro- d -ribitol (green), and the re-docked ligand (red); ( c ) human cathepsin K (HsCatK, PDB 1U9V [ 38 ]) showing the co-crystallized ligand, 6-(cyclohexylamino)-9-[2-(4-methylpiperazin-1-yl)-ethyl]-9 H -purine-2-carbonitrile (green), and the re-docked ligand (blue); and ( d ) human cathepsin L (HsCatL, PDB 3HWN [ 39 ]) showing the co-crystallized ligand, N -α-[(3- t -Butyl-1-methyl-1 H -pyrazol-5-yl)carbonyl]- N -[(2 E )-2-iminoethyl]-3-{5-[( Z )-iminomethyl]-1,3,4-oxadiazol-2-yl}- l -phenylalaninamide (green), and the re-docked ligand (aqua).

    Article Snippet: Homology Modeling Homology models for each of the Trichomonas proteins that are not currently available from the Protein Data Bank (PDB) were constructed from crystal structure templates found in the Protein Data Bank using FASTA sequences downloaded from the National Center for Biotechnology Information’s (NCBI) GenBank.

    Techniques:

    Overlay of the protein structures of rabbit ( Oryctolagus cuniculus ) cathepsin K, PDB 2F7D [ 25 ] (red ribbon), and the homology model of Trichomonas vaginalis papain-like protein, TvCP2 (blue ribbon). The co-crystallized ligand is shown as a wireframe structure.

    Journal: Scientia Pharmaceutica

    Article Title: Natural Products as New Treatment Options for Trichomoniasis: A Molecular Docking Investigation

    doi: 10.3390/scipharm85010005

    Figure Lengend Snippet: Overlay of the protein structures of rabbit ( Oryctolagus cuniculus ) cathepsin K, PDB 2F7D [ 25 ] (red ribbon), and the homology model of Trichomonas vaginalis papain-like protein, TvCP2 (blue ribbon). The co-crystallized ligand is shown as a wireframe structure.

    Article Snippet: Homology Modeling Homology models for each of the Trichomonas proteins that are not currently available from the Protein Data Bank (PDB) were constructed from crystal structure templates found in the Protein Data Bank using FASTA sequences downloaded from the National Center for Biotechnology Information’s (NCBI) GenBank.

    Techniques:

    Expression levels and signaling capacities of WT and R753Q YFP-TLR2 species. A–D , HEK293 cells were transiently ( A , C , and D ) or stably ( B ) transfected with expression vectors encoding WT or R753Q YFP-TLR2 variants. A , after recovery for 48 h,

    Journal: The Journal of Biological Chemistry

    Article Title: R753Q Polymorphism Inhibits Toll-like Receptor (TLR) 2 Tyrosine Phosphorylation, Dimerization with TLR6, and Recruitment of Myeloid Differentiation Primary Response Protein 88 *

    doi: 10.1074/jbc.M112.375493

    Figure Lengend Snippet: Expression levels and signaling capacities of WT and R753Q YFP-TLR2 species. A–D , HEK293 cells were transiently ( A , C , and D ) or stably ( B ) transfected with expression vectors encoding WT or R753Q YFP-TLR2 variants. A , after recovery for 48 h,

    Article Snippet: Structural models of the WT and R753Q-containing TIR domains of TLR2 were built using the WT TLR2 structure (Protein Data Bank (PDB) accession code 1FYW ) and the 3D-JIGSAW Protein Comparative Modeling Server (version 2.0) and visualized and analyzed using the Cn3D 4.3 macromolecular structure viewer (National Center for Biotechnology Information (NCBI), ) and PyMOL.

    Techniques: Expressing, Stable Transfection, Transfection

    The effect of R753Q polymorphism on TLR2-elicited cytokine gene expression. A , HEK293 cells stably transfected with plasmids encoding WT or R753Q YFP-TLR2 were treated for 3 h with medium, 1 μg/ml Pam3Cys, or 5 μg/ml M. tuberculosis (

    Journal: The Journal of Biological Chemistry

    Article Title: R753Q Polymorphism Inhibits Toll-like Receptor (TLR) 2 Tyrosine Phosphorylation, Dimerization with TLR6, and Recruitment of Myeloid Differentiation Primary Response Protein 88 *

    doi: 10.1074/jbc.M112.375493

    Figure Lengend Snippet: The effect of R753Q polymorphism on TLR2-elicited cytokine gene expression. A , HEK293 cells stably transfected with plasmids encoding WT or R753Q YFP-TLR2 were treated for 3 h with medium, 1 μg/ml Pam3Cys, or 5 μg/ml M. tuberculosis (

    Article Snippet: Structural models of the WT and R753Q-containing TIR domains of TLR2 were built using the WT TLR2 structure (Protein Data Bank (PDB) accession code 1FYW ) and the 3D-JIGSAW Protein Comparative Modeling Server (version 2.0) and visualized and analyzed using the Cn3D 4.3 macromolecular structure viewer (National Center for Biotechnology Information (NCBI), ) and PyMOL.

    Techniques: Expressing, Stable Transfection, Transfection

    Molecular modeling of the structures of the TIR domains of WT and R753Q TIR2 species. A–C , ribbon models of WT Arg-753 ( A ) and mutant Gln-753 ( MUT Q753 ) ( B ) TIR domains of TLR2 and their overlay ( C ) are shown. D , a close-up of the DD-loop-αD

    Journal: The Journal of Biological Chemistry

    Article Title: R753Q Polymorphism Inhibits Toll-like Receptor (TLR) 2 Tyrosine Phosphorylation, Dimerization with TLR6, and Recruitment of Myeloid Differentiation Primary Response Protein 88 *

    doi: 10.1074/jbc.M112.375493

    Figure Lengend Snippet: Molecular modeling of the structures of the TIR domains of WT and R753Q TIR2 species. A–C , ribbon models of WT Arg-753 ( A ) and mutant Gln-753 ( MUT Q753 ) ( B ) TIR domains of TLR2 and their overlay ( C ) are shown. D , a close-up of the DD-loop-αD

    Article Snippet: Structural models of the WT and R753Q-containing TIR domains of TLR2 were built using the WT TLR2 structure (Protein Data Bank (PDB) accession code 1FYW ) and the 3D-JIGSAW Protein Comparative Modeling Server (version 2.0) and visualized and analyzed using the Cn3D 4.3 macromolecular structure viewer (National Center for Biotechnology Information (NCBI), ) and PyMOL.

    Techniques: Mutagenesis

    The impact of R753Q polymorphism on TLR2-mediated phosphorylation of p38 and IκB-α and degradation of IκB-α. WT or R753Q YFP-TLR2 variants were overexpressed in HEK293T cells following transient transfection of the corresponding

    Journal: The Journal of Biological Chemistry

    Article Title: R753Q Polymorphism Inhibits Toll-like Receptor (TLR) 2 Tyrosine Phosphorylation, Dimerization with TLR6, and Recruitment of Myeloid Differentiation Primary Response Protein 88 *

    doi: 10.1074/jbc.M112.375493

    Figure Lengend Snippet: The impact of R753Q polymorphism on TLR2-mediated phosphorylation of p38 and IκB-α and degradation of IκB-α. WT or R753Q YFP-TLR2 variants were overexpressed in HEK293T cells following transient transfection of the corresponding

    Article Snippet: Structural models of the WT and R753Q-containing TIR domains of TLR2 were built using the WT TLR2 structure (Protein Data Bank (PDB) accession code 1FYW ) and the 3D-JIGSAW Protein Comparative Modeling Server (version 2.0) and visualized and analyzed using the Cn3D 4.3 macromolecular structure viewer (National Center for Biotechnology Information (NCBI), ) and PyMOL.

    Techniques: Transfection

    The R753Q polymorphism impairs the ability of TLR2 to hetero-dimerize with TLR6 upon Pam2Cys stimulation. A , 293/YFP-TLR2 stable cell lines expressing WT or R753Q YFP-TLR2 variants were co-transfected with pcDNA3-CFP-TLR6. After recovery for 20 h, cells

    Journal: The Journal of Biological Chemistry

    Article Title: R753Q Polymorphism Inhibits Toll-like Receptor (TLR) 2 Tyrosine Phosphorylation, Dimerization with TLR6, and Recruitment of Myeloid Differentiation Primary Response Protein 88 *

    doi: 10.1074/jbc.M112.375493

    Figure Lengend Snippet: The R753Q polymorphism impairs the ability of TLR2 to hetero-dimerize with TLR6 upon Pam2Cys stimulation. A , 293/YFP-TLR2 stable cell lines expressing WT or R753Q YFP-TLR2 variants were co-transfected with pcDNA3-CFP-TLR6. After recovery for 20 h, cells

    Article Snippet: Structural models of the WT and R753Q-containing TIR domains of TLR2 were built using the WT TLR2 structure (Protein Data Bank (PDB) accession code 1FYW ) and the 3D-JIGSAW Protein Comparative Modeling Server (version 2.0) and visualized and analyzed using the Cn3D 4.3 macromolecular structure viewer (National Center for Biotechnology Information (NCBI), ) and PyMOL.

    Techniques: Stable Transfection, Expressing, Transfection

    R753Q TLR2 shows deficient capacity to recruit Mal and MyD88 in response to agonist stimulation. HEK293T cells were transiently transfected with pEFBOS-Flag-Mal ( A ) or pcDNA3-AU1-MyD88 ( B ) in combination with pcDNA3-WT YFP-TLR2 or pcDNA3-R753Q YFP-TLR2,

    Journal: The Journal of Biological Chemistry

    Article Title: R753Q Polymorphism Inhibits Toll-like Receptor (TLR) 2 Tyrosine Phosphorylation, Dimerization with TLR6, and Recruitment of Myeloid Differentiation Primary Response Protein 88 *

    doi: 10.1074/jbc.M112.375493

    Figure Lengend Snippet: R753Q TLR2 shows deficient capacity to recruit Mal and MyD88 in response to agonist stimulation. HEK293T cells were transiently transfected with pEFBOS-Flag-Mal ( A ) or pcDNA3-AU1-MyD88 ( B ) in combination with pcDNA3-WT YFP-TLR2 or pcDNA3-R753Q YFP-TLR2,

    Article Snippet: Structural models of the WT and R753Q-containing TIR domains of TLR2 were built using the WT TLR2 structure (Protein Data Bank (PDB) accession code 1FYW ) and the 3D-JIGSAW Protein Comparative Modeling Server (version 2.0) and visualized and analyzed using the Cn3D 4.3 macromolecular structure viewer (National Center for Biotechnology Information (NCBI), ) and PyMOL.

    Techniques: Transfection

    The impact of R753Q polymorphism on agonist-induced tyrosine phosphorylation of TLR2. A and B , HEK293 stable transfectants expressing WT or R753Q TLR2 were stimulated for the indicated time points with 100 ng/ml Pam3Cys ( A ) or treated for 15 min with

    Journal: The Journal of Biological Chemistry

    Article Title: R753Q Polymorphism Inhibits Toll-like Receptor (TLR) 2 Tyrosine Phosphorylation, Dimerization with TLR6, and Recruitment of Myeloid Differentiation Primary Response Protein 88 *

    doi: 10.1074/jbc.M112.375493

    Figure Lengend Snippet: The impact of R753Q polymorphism on agonist-induced tyrosine phosphorylation of TLR2. A and B , HEK293 stable transfectants expressing WT or R753Q TLR2 were stimulated for the indicated time points with 100 ng/ml Pam3Cys ( A ) or treated for 15 min with

    Article Snippet: Structural models of the WT and R753Q-containing TIR domains of TLR2 were built using the WT TLR2 structure (Protein Data Bank (PDB) accession code 1FYW ) and the 3D-JIGSAW Protein Comparative Modeling Server (version 2.0) and visualized and analyzed using the Cn3D 4.3 macromolecular structure viewer (National Center for Biotechnology Information (NCBI), ) and PyMOL.

    Techniques: Expressing

    R753Q TLR2 mediates impaired activation of NF-κB luciferase reporter in response to inactivated M. tuberculosis , S. aureus , mycobacteria-derived cell wall, and culture filtrate fractions, LAM and Pam3Cys. HEK293T cells were transiently transfected

    Journal: The Journal of Biological Chemistry

    Article Title: R753Q Polymorphism Inhibits Toll-like Receptor (TLR) 2 Tyrosine Phosphorylation, Dimerization with TLR6, and Recruitment of Myeloid Differentiation Primary Response Protein 88 *

    doi: 10.1074/jbc.M112.375493

    Figure Lengend Snippet: R753Q TLR2 mediates impaired activation of NF-κB luciferase reporter in response to inactivated M. tuberculosis , S. aureus , mycobacteria-derived cell wall, and culture filtrate fractions, LAM and Pam3Cys. HEK293T cells were transiently transfected

    Article Snippet: Structural models of the WT and R753Q-containing TIR domains of TLR2 were built using the WT TLR2 structure (Protein Data Bank (PDB) accession code 1FYW ) and the 3D-JIGSAW Protein Comparative Modeling Server (version 2.0) and visualized and analyzed using the Cn3D 4.3 macromolecular structure viewer (National Center for Biotechnology Information (NCBI), ) and PyMOL.

    Techniques: Activation Assay, Luciferase, Derivative Assay, Laser Capture Microdissection, Transfection