This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2nl8

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:28, 3 April 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2nl8.gif|left|200px]]<br /><applet load="2nl8" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2nl8, resolution 2.30&Aring;" />
 
-
'''The origin binding domain of the SV40 large T antigen bound non specifically to a 17 bp palindrome DNA (sites 1 and 3)'''<br />
 
-
==Overview==
+
==The origin binding domain of the SV40 large T antigen bound non specifically to a 17 bp palindrome DNA (sites 1 and 3)==
-
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.
+
<StructureSection load='2nl8' size='340' side='right'caption='[[2nl8]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 +
== Structural highlights ==
 +
<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>
 +
</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>
 +
<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>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q98ZP7_SV40 Q98ZP7_SV40]
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nl/2nl8_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
2NL8 is a [http://en.wikipedia.org/wiki/Single_protein 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].
+
*[[Large T Antigen|Large T Antigen]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=17139255 17139255]
+
[[Category: Large Structures]]
-
[[Category: Simian virus 40]]
+
[[Category: Macaca mulatta polyomavirus 1]]
-
[[Category: Single protein]]
+
[[Category: Bochkarev A]]
-
[[Category: Bochkarev, A.]]
+
[[Category: Bochkareva E]]
-
[[Category: Bochkareva, E.]]
+
[[Category: Martynowski D]]
-
[[Category: Martynowski, D.]]
+
-
[[Category: dna binding protein]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:08:10 2008''
+

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

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2nl8"
Personal tools