1sva

From Proteopedia

(Difference between revisions)

Revision as of 16:40, 10 April 2020

SIMIAN VIRUS 40

1sva, resolution 3.10Å

Structural highlights

1sva is a 6 chain structure with sequence from Simian virus 40. The November 2003 RCSB PDB Molecule of the Month feature on Simian Virus 40 by David S. Goodsell is 10.2210/rcsb_pdb/mom_2003_11. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[VP1_SV40] Forms an icosahedral capsid with a T=7 symmetry and a 40 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with VP2 or VP3 proteins. Binds to N-glycolylneuraminic analog of the ganglioside GM1 on the cell surface to provide virion attachment to target cell. Once attached, the virion is internalized by caveolin-mediated endocytosis and traffics to the endoplasmic reticulum. Inside the endoplasmic reticulum, the protein folding machinery isomerizes VP1 interpentamer disulfide bonds, thereby triggering initial uncoating. Next, the virion uses the endoplasmic reticulum-associated degradation machinery to probably translocate in the cytosol before reaching the nucleus. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2/Vp3 nuclear localization signal. The assembly takes place in the cell nucleus. Encapsulates the genomic DNA and participates in rearranging nucleosomes around the viral DNA. The viral progenies exit the cells by lytic release.

Evolutionary Conservation

Checkto colour the structure by Evolutionary Conservation, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

BACKGROUND: The structure of simian virus 40 (SV40), previously determined at 3.8 degree resolution, shows how its pentameric VP1 assembly units are tied together by extended C-terminal arms. In order to define more precisely the possible assembly mechanisms, we have refined the structure at 3.1 degree resolution. RESULTS: New data from a high-intensity synchrotron source have been used for phase extension by electron-density averaging and refinement, exploiting only the strict 5-fold non-crystallographic symmetry for the real-space averaging steps. The accurate model enables us to study important structural features of the virus particle in detail. The remarkably invariant core of the VP1 pentamer bears the docking sites for the C-terminal arms from other pentamers. These contacts are the principal way in which pentameric assembly units are linked together in the capsid. Only at the interface between five-coordinated and six-coordinated pentamers do the pentamer cores appear to interact strongly. There are two cation-binding sites per VP1 monomer, seen in a soaking experiment with gadolinium nitrate. These sites are quite close to each other at the interfaces between pentamers. CONCLUSION: We propose that the contact between five-coordinated and six-coordinated pentamers may help to generate a six-pentamer nucleus, with which further pentamers can assemble to generate the complete particle. Calcium ions probably stabilize the structure of the assembled particle, rather than direct its assembly.

The structure of simian virus 40 refined at 3.1 A resolution.,Stehle T, Gamblin SJ, Yan Y, Harrison SC Structure. 1996 Feb 15;4(2):165-82. PMID:8805523^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Stehle T, Gamblin SJ, Yan Y, Harrison SC. The structure of simian virus 40 refined at 3.1 A resolution. Structure. 1996 Feb 15;4(2):165-82. PMID:8805523

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1sva"

@@ Line 3: / Line 3: @@
 <SX load='1sva' size='340' side='right' viewer='molstar' caption='[[1sva]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1sva]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Simian_virus_40 Simian virus 40]. The November 2003 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Simian Virus 40''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2003_11 10.2210/rcsb_pdb/mom_2003_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SVA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SVA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1sva]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Simian_virus_40 Simian virus 40]. The November 2003 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Simian Virus 40''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2003_11 10.2210/rcsb_pdb/mom_2003_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SVA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1SVA FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1sva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sva OCA], [http://pdbe.org/1sva PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sva RCSB], [http://www.ebi.ac.uk/pdbsum/1sva PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sva ProSAT]</span></td></tr>
+</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=1sva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sva OCA], [http://pdbe.org/1sva PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sva RCSB], [http://www.ebi.ac.uk/pdbsum/1sva PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sva ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 32: / Line 32: @@
 *[[Jmol/Visualizing large molecules|Jmol/Visualizing large molecules]]
 *[[SV40 Capsid Simplified|SV40 Capsid Simplified]]
-*[[Virus coat protein|Virus coat protein]]
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
 == References ==
 <references/>

1sva

From Proteopedia

Revision as of 16:40, 10 April 2020

SIMIAN VIRUS 40

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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