2gh8: Difference between revisions

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<SX load='2gh8' size='340' side='right' viewer='molstar' caption='[[2gh8]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
<SX load='2gh8' size='340' side='right' viewer='molstar' caption='[[2gh8]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2gh8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/San_miguel_sea_lion_virus_4 San miguel sea lion virus 4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GH8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GH8 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2gh8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/San_Miguel_sea_lion_virus_4 San Miguel sea lion virus 4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GH8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GH8 FirstGlance]. <br>
</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=2gh8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gh8 OCA], [https://pdbe.org/2gh8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gh8 RCSB], [https://www.ebi.ac.uk/pdbsum/2gh8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gh8 ProSAT]</span></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]] 3.2&#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=2gh8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gh8 OCA], [https://pdbe.org/2gh8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gh8 RCSB], [https://www.ebi.ac.uk/pdbsum/2gh8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gh8 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/CAPSD_SMSV4 CAPSD_SMSV4]] 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 to feline junctional adhesion molecule A (F11R) and/or to alpha-2,6-linked sialic acid. Once attached, the virion is endocytosed. Acidification of the endosome induces conformational change of capsid protein thereby injecting virus genomic RNA into host cytoplasm (By similarity).  
[https://www.uniprot.org/uniprot/CAPSD_SMSV4 CAPSD_SMSV4] 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 to feline junctional adhesion molecule A (F11R) and/or to alpha-2,6-linked sialic acid. Once attached, the virion is endocytosed. Acidification of the endosome induces conformational change of capsid protein thereby injecting virus genomic RNA into host cytoplasm (By similarity).
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[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=2gh8 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=2gh8 ConSurf].
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== Publication Abstract from PubMed ==
Caliciviruses, grouped into four genera, are important human and veterinary pathogens with a potential for zoonosis. In these viruses, capsid-related functions such as assembly, antigenicity, and receptor interactions are predominantly encoded in a single protein that forms an icosahedral capsid. Understanding of the immunologic functions and pathogenesis of human caliciviruses in the Norovirus and Sapovirus genera is hampered by the lack of a cell culture system or animal models. Much of our understanding of these viruses, including the structure, has depended on recombinant capsids. Here we report the atomic structure of a native calicivirus from the Vesivirus genus that exhibits a broad host range possibly including humans and map immunological function onto a calicivirus structure. The vesivirus structure, despite a similar architectural design as seen in the recombinant norovirus capsid, exhibits novel features and indicates how the unique modular organization of the capsid protein with interdomain flexibility, similar to an antibody structure with a hinge and an elbow, integrates capsid-related functions and facilitates strain diversity in caliciviruses. The internally located N-terminal arm participates in a novel network of interactions through domain swapping to assist the assembly of the shell domain into an icosahedral scaffold, from which the protruding domain emanates. Neutralization epitopes localize to three hypervariable loops in the distal portion of the protruding domain surrounding a region that exhibits host-specific conservation. These observations suggest a mechanism for antigenic diversity and host specificity in caliciviruses and provide a structural framework for vaccine development.
X-ray structure of a native calicivirus: structural insights into antigenic diversity and host specificity.,Chen R, Neill JD, Estes MK, Prasad BV Proc Natl Acad Sci U S A. 2006 May 23;103(21):8048-53. Epub 2006 May 15. PMID:16702551<ref>PMID:16702551</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2gh8" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
== References ==
<references/>
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__TOC__
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[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: San miguel sea lion virus 4]]
[[Category: San Miguel sea lion virus 4]]
[[Category: Chen, R]]
[[Category: Chen R]]
[[Category: Domain swapping]]
[[Category: Icosahedral t=3 capsid]]
[[Category: Icosahedral virus]]
[[Category: N-terminal arm]]
[[Category: Native calicivirus]]
[[Category: Protruding domain]]
[[Category: Shell domain]]
[[Category: Vesivirus]]
[[Category: Virus]]

Latest revision as of 12:27, 14 February 2024

X-ray structure of a native calicivirusX-ray structure of a native calicivirus

2gh8, resolution 3.20Å

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OCA
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