3d26

From Proteopedia

(Difference between revisions)

Revision as of 14:52, 11 August 2016

Norwalk P domain A-trisaccharide complex

Structural highlights

3d26 is a 2 chain structure with sequence from Norwalk virus. This structure supersedes the now removed PDB entry 3by3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	1ihm, 3by1, 3by2
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[CAPSD_NVN68] Capsid protein self assembles to form an icosahedral capsid with a T=3 symmetry, about 38 nm in diameter, and consisting of 180 capsid proteins. A smaller form of capsid with a diameter of 23 nm might be capsid proteins assembled as icosahedron with T=1 symmetry. The capsid encapsulate the genomic RNA and VP2 proteins. Attaches virion to target cells by binding histo-blood group antigens present on gastroduodenal epithelial cells.^[1] Soluble capsid protein may play a role in viral immunoevasion.^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Noroviruses are positive-sense, single-stranded RNA viruses that cause acute gastroenteritis. They recognize human histo-blood group antigens as receptors in a strain-specific manner. The structures presented here were analyzed in order to elucidate the structural basis for differences in ligand recognition of noroviruses from different genogroups, the prototypic Norwalk virus (NV; GI-1) and VA387 (GII-4), which recognize the same A antigen but differ in that NV is unable to bind to the B antigen. Two forms of the receptor-binding domain of the norovirus coat protein, the P domain and the P polypeptide, that were previously shown to differ in receptor binding and P-particle formation properties were studied. Comparison of the structures of the NV P domain with and without A trisaccharide and the NV P polypeptide revealed no major ligand-induced changes. The 2.3-A cocrystal structure reveals that the A trisaccharide binds to the NV P domain through interactions with the residues Ser377, Asp327, His329, and Ser380 in a mode distinct from that previously reported for the VA387 P-domain-A-trisaccharide complex. Mutational analyses confirm the importance of these residues in NV P-particle binding to native A antigen. The alpha-GalNAc residue unique to the A trisaccharide is buried deeply in the NV binding pocket, unlike in the structures of A and B trisaccharides bound to VA387 P domain, where the alpha-fucose residue forms the most protein contacts. The A-trisaccharide binding mode seen in the NV P domain complex cannot be sterically accommodated in the VA387 P domain.

Structural basis for the receptor binding specificity of Norwalk virus.,Bu W, Mamedova A, Tan M, Xia M, Jiang X, Hegde RS J Virol. 2008 Jun;82(11):5340-7. Epub 2008 Apr 2. PMID:18385236^[3]

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

References

↑ Tan M, Meller J, Jiang X. C-terminal arginine cluster is essential for receptor binding of norovirus capsid protein. J Virol. 2006 Aug;80(15):7322-31. PMID:16840313 doi:http://dx.doi.org/80/15/7322
↑ Tan M, Meller J, Jiang X. C-terminal arginine cluster is essential for receptor binding of norovirus capsid protein. J Virol. 2006 Aug;80(15):7322-31. PMID:16840313 doi:http://dx.doi.org/80/15/7322
↑ Bu W, Mamedova A, Tan M, Xia M, Jiang X, Hegde RS. Structural basis for the receptor binding specificity of Norwalk virus. J Virol. 2008 Jun;82(11):5340-7. Epub 2008 Apr 2. PMID:18385236 doi:10.1128/JVI.00135-08

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/3d26"

Categories: Norwalk virus | Bu, W | Hegde, R | Norwalk p domain a trisaccaride complex | Viral protein

@@ Line 1: / Line 1: @@
 ==Norwalk P domain A-trisaccharide complex==
 <StructureSection load='3d26' size='340' side='right' caption='[[3d26]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ihm|1ihm]], [[3by1|3by1]], [[3by2|3by2]]</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=3d26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d26 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d26 RCSB], [http://www.ebi.ac.uk/pdbsum/3d26 PDBsum]</span></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=3d26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d26 OCA], [http://pdbe.org/3d26 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d26 RCSB], [http://www.ebi.ac.uk/pdbsum/3d26 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3d26 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[[http://www.uniprot.org/uniprot/CAPSD_NVN68 CAPSD_NVN68]] Capsid protein self assembles to form an icosahedral capsid with a T=3 symmetry, about 38 nm in diameter, and consisting of 180 capsid proteins. A smaller form of capsid with a diameter of 23 nm might be capsid proteins assembled as icosahedron with T=1 symmetry. The capsid encapsulate the genomic RNA and VP2 proteins. Attaches virion to target cells by binding histo-blood group antigens present on gastroduodenal epithelial cells.<ref>PMID:16840313</ref>   Soluble capsid protein may play a role in viral immunoevasion.<ref>PMID:16840313</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 15: / Line 18: @@
     <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3d26 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3d26" style="background-color:#fffaf0;"></div>
 ==See Also==

3d26

From Proteopedia

Revision as of 14:52, 11 August 2016

Norwalk P domain A-trisaccharide complex

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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