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3vwb

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Current revision (08:42, 20 March 2024) (edit) (undo)
 
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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3vwb]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Shigella_flexneri_2a Shigella flexneri 2a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VWB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VWB FirstGlance]. <br>
<table><tr><td colspan='2'>[[3vwb]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Shigella_flexneri_2a Shigella flexneri 2a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VWB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VWB FirstGlance]. <br>
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</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.416&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ntz|2ntz]], [[1zx4|1zx4]], [[3mkz|3mkz]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">virB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=42897 Shigella flexneri 2a])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vwb OCA], [https://pdbe.org/3vwb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vwb RCSB], [https://www.ebi.ac.uk/pdbsum/3vwb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vwb ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vwb OCA], [https://pdbe.org/3vwb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vwb RCSB], [https://www.ebi.ac.uk/pdbsum/3vwb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vwb ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/VIRB_SHIFL VIRB_SHIFL]] Transcription activator for the invasion antigens IpaB, IpaC and IpaD. VirB is itself regulated by VirF.
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[https://www.uniprot.org/uniprot/VIRB_SHIFL VIRB_SHIFL] Transcription activator for the invasion antigens IpaB, IpaC and IpaD. VirB is itself regulated by VirF.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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VirB activates transcription of virulence genes in Shigella flexneri by alleviating heat-stable nucleoid-structuring protein-mediated promoter repression. VirB is unrelated to the conventional transcriptional regulators, but homologous to the plasmid partitioning proteins. We determined the crystal structures of VirB HTH domain bound by the cis-acting site containing the inverted repeat, revealing that the VirB-DNA complex is related to ParB-ParS-like complexes, presenting an example that a ParB-like protein acts exclusively in transcriptional regulation. The HTH domain of VirB docks DNA major groove and provides multiple contacts to backbone and bases, in which the only specific base readout is mediated by R167. VirB only recognizes one half site of the inverted repeats containing the most matches to the consensus for VirB binding. The binding of VirB induces DNA conformational changes and introduces a bend at an invariant A-tract segment in the cis-acting site, suggesting a role of DNA remodeling. VirB exhibits positive cooperativity in DNA binding that is contributed by the C-terminal domain facilitating VirB oligomerization. The isolated HTH domain only confers partial DNA specificity. Additional determinants for sequence specificity may reside in N- or C-terminal domains. Collectively, our findings support and extend a previously proposed model for relieving heat-stable nucleoid-structuring protein-mediated repression by VirB.
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Structural insights into VirB-DNA complexes reveal mechanism of transcriptional activation of virulence genes.,Gao X, Zou T, Mu Z, Qin B, Yang J, Waltersperger S, Wang M, Cui S, Jin Q Nucleic Acids Res. 2013 Dec 1;41(22):10529-41. doi: 10.1093/nar/gkt748. Epub 2013, Aug 27. PMID:23985969<ref>PMID:23985969</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3vwb" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]]
*[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Shigella flexneri 2a]]
[[Category: Shigella flexneri 2a]]
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[[Category: Cui, S]]
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[[Category: Cui S]]
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[[Category: Gao, X P]]
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[[Category: Gao XP]]
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[[Category: Waltersperger, S]]
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[[Category: Waltersperger S]]
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[[Category: Wang, M T]]
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[[Category: Wang MT]]
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[[Category: Dsdna]]
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[[Category: Hth dna binding motif]]
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[[Category: Hth dna-binding motif]]
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[[Category: Palindromic dna sequence]]
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[[Category: Parb like]]
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[[Category: Sequence specific dsdna binding]]
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[[Category: Transcription-dna complex]]
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[[Category: Transcriptional activator]]
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Current revision

Crystal structure of VirB core domain (Se-Met derivative) complexed with the cis-acting site (5-BRU modifications) upstream icsb promoter

PDB ID 3vwb

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