1r8h: Difference between revisions

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 <StructureSection load='1r8h' size='340' side='right'caption='[[1r8h]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1r8h]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Hpv6a Hpv6a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R8H OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1R8H FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1r8h]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_papillomavirus_type_6a Human papillomavirus type 6a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R8H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R8H FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">E2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37122 HPV6A])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1r8h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r8h OCA], [http://pdbe.org/1r8h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1r8h RCSB], [http://www.ebi.ac.uk/pdbsum/1r8h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1r8h 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=1r8h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r8h OCA], [https://pdbe.org/1r8h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r8h RCSB], [https://www.ebi.ac.uk/pdbsum/1r8h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r8h ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/VE2_HPV6A VE2_HPV6A]] E2 regulates viral transcription and DNA replication. It binds to the E2RE response element (5'-ACCNNNNNNGGT-3') present in multiple copies in the regulatory region. It can either activate or repress transcription depending on E2RE's position with regards to proximal promoter elements. Repression occurs by sterically hindering the assembly of the transcription initiation complex. The E1-E2 complex binds to the origin of DNA replication.
+[https://www.uniprot.org/uniprot/VE2_HPV6A VE2_HPV6A] E2 regulates viral transcription and DNA replication. It binds to the E2RE response element (5'-ACCNNNNNNGGT-3') present in multiple copies in the regulatory region. It can either activate or repress transcription depending on E2RE's position with regards to proximal promoter elements. Repression occurs by sterically hindering the assembly of the transcription initiation complex. The E1-E2 complex binds to the origin of DNA replication.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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 </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1r8h ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Human papillomaviruses (HPVS) that infect the genital tract can be divided into two groups: high-risk HPV types, such as HPV 16 and HPV 18, are associated with cancer, low-risk HPV types, such as HPV 6, are associated with benign warts. In both high-risk and low-risk HPV types, the papillomavirus E2 protein binds to four sites within the viral long control region (LCR) and regulates viral gene expression. Here, we present the crystal structure of the minimal DNA-binding domain (DBD) from the HPV 6 E2 protein. We show that the HPV 6 E2 DBD is structurally more similar to the HPV 18 and bovine papillomavirus type 1 (BPV1) E2 proteins than it is to the HPV 16 E2 protein. Using gel retardation assays, we show that the hierarchy of E2 sites within the HPV 16 and HPV 6 LCRs are different. However, despite these differences in structure and site preference, both the HPV 16 and 6 E2 DBDs recognise an extended version of the consensus E2 binding site derived from studies of the BPV1 E2 protein. In both cases, the preferred binding site is 5'AACCGN(4)CGGTT3', where the additional flanking base-pairs are in bold and N(4) represents a four base-pair central spacer. Both of these HPV proteins bind preferentially to E2 sites that contain an A:T-rich central spacer. We show that the preference for an A:T-rich central spacer is due, at least in part, to the need to adopt a DNA conformation that facilitates protein contacts with the flanking base-pairs.
-Comparison of the structure and DNA-binding properties of the E2 proteins from an oncogenic and a non-oncogenic human papillomavirus.,Dell G, Wilkinson KW, Tranter R, Parish J, Leo Brady R, Gaston K J Mol Biol. 2003 Dec 12;334(5):979-91. PMID:14643661<ref>PMID:14643661</ref>
+==See Also==
+*[[Regulatory protein E2|Regulatory protein E2]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1r8h" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Hpv6a]]
+[[Category: Human papillomavirus type 6a]]
 [[Category: Large Structures]]
-[[Category: Brady, R L]]
+[[Category: Brady RL]]
-[[Category: Dell, G]]
+[[Category: Dell G]]
-[[Category: Gaston, K]]
+[[Category: Gaston K]]
-[[Category: Parish, J]]
+[[Category: Parish J]]
-[[Category: Tranter, R]]
+[[Category: Tranter R]]
-[[Category: Wilkinson, K W]]
+[[Category: Wilkinson KW]]
-[[Category: Anti-parallel beta-barrel]]
-[[Category: Dna-binding domain]]
-[[Category: Replication]]
-[[Category: Transcription]]