2nl8

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[[Image:2nl8.gif|left|200px]]
 
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{{Structure
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==The origin binding domain of the SV40 large T antigen bound non specifically to a 17 bp palindrome DNA (sites 1 and 3)==
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|PDB= 2nl8 |SIZE=350|CAPTION= <scene name='initialview01'>2nl8</scene>, resolution 2.30&Aring;
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<StructureSection load='2nl8' size='340' side='right'caption='[[2nl8]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
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<table><tr><td colspan='2'>[[2nl8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Macaca_mulatta_polyomavirus_1 Macaca mulatta polyomavirus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NL8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NL8 FirstGlance]. <br>
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|ACTIVITY=
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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]] 2.3&#8491;</td></tr>
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|GENE= large T antigen ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10633 Simian virus 40])
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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=2nl8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nl8 OCA], [https://pdbe.org/2nl8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nl8 RCSB], [https://www.ebi.ac.uk/pdbsum/2nl8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nl8 ProSAT]</span></td></tr>
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|DOMAIN=
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</table>
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|RELATEDENTRY=[[2ipr|2IPR]], [[2itj|2ITJ]], [[2itl|2ITL]]
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== Function ==
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2nl8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nl8 OCA], [http://www.ebi.ac.uk/pdbsum/2nl8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2nl8 RCSB]</span>
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[https://www.uniprot.org/uniprot/Q98ZP7_SV40 Q98ZP7_SV40]
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}}
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nl/2nl8_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=2nl8 ConSurf].
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<div style="clear:both"></div>
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'''The origin binding domain of the SV40 large T antigen bound non specifically to a 17 bp palindrome DNA (sites 1 and 3)'''
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==See Also==
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*[[Large T Antigen|Large T Antigen]]
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__TOC__
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==Overview==
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</StructureSection>
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The large T antigen (T-ag) protein binds to and activates DNA replication from the origin of DNA replication (ori) in simian virus 40 (SV40). Here, we determined the crystal structures of the T-ag origin-binding domain (OBD) in apo form, and bound to either a 17 bp palindrome (sites 1 and 3) or a 23 bp ori DNA palindrome comprising all four GAGGC binding sites for OBD. The T-ag OBDs were shown to interact with the DNA through a loop comprising Ser147-Thr155 (A1 loop), a combination of a DNA-binding helix and loop (His203-Asn210), and Asn227. The A1 loop traveled back-and-forth along the major groove and accounted for most of the sequence-determining contacts with the DNA. Unexpectedly, in both T-ag-DNA structures, the T-ag OBDs bound DNA independently and did not make direct protein-protein contacts. The T-ag OBD was also captured bound to a non-consensus site ATGGC even in the presence of its canonical site GAGGC. Our observations taken together with the known biochemical and structural features of the T-ag-origin interaction suggest a model for origin unwinding.
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[[Category: Large Structures]]
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[[Category: Macaca mulatta polyomavirus 1]]
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==About this Structure==
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[[Category: Bochkarev A]]
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2NL8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Simian_virus_40 Simian virus 40]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NL8 OCA].
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[[Category: Bochkareva E]]
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[[Category: Martynowski D]]
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==Reference==
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Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA., Bochkareva E, Martynowski D, Seitova A, Bochkarev A, EMBO J. 2006 Dec 13;25(24):5961-9. Epub 2006 Nov 30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17139255 17139255]
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[[Category: Simian virus 40]]
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[[Category: Single protein]]
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[[Category: Bochkarev, A.]]
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[[Category: Bochkareva, E.]]
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[[Category: Martynowski, D.]]
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[[Category: dna binding protein]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:04:47 2008''
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Current revision

The origin binding domain of the SV40 large T antigen bound non specifically to a 17 bp palindrome DNA (sites 1 and 3)

PDB ID 2nl8

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