View source for 3j3y


==Atomic-level structure of the entire HIV-1 capsid (186 hexamers + 12 pentamers)==
<SX load='3j3y' size='340' side='right' viewer='molstar' caption='[[3j3y]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3j3y]] is a 1176 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vuu 1vuu], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vuv 1vuv], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vuw 1vuw], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vux 1vux], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vuy 1vuy], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vuz 1vuz], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vv0 1vv0], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vv1 1vv1], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vv2 1vv2], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vv3 1vv3], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vv4 1vv4], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vv5 1vv5], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vv6 1vv6], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vv7 1vv7], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vv8 1vv8], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vv9 1vv9], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vva 1vva], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vvb 1vvb], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vvf 1vvf], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vvg 1vvg], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vvh 1vvh] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vvi 1vvi]. The July 2013 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''HIV Capsid''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2013_7 10.2210/rcsb_pdb/mom_2013_7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J3Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J3Y FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy</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=3j3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j3y OCA], [https://pdbe.org/3j3y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j3y RCSB], [https://www.ebi.ac.uk/pdbsum/3j3y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j3y ProSAT]</span></td></tr>
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== Function ==
[https://www.uniprot.org/uniprot/Q79791_9HIV1 Q79791_9HIV1] Capsid protein p24 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex (By similarity).[SAAS:SAAS000071_004_008806]  Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers (By similarity).[SAAS:SAAS000071_004_011858]
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== Publication Abstract from PubMed ==
Retroviral capsid proteins are conserved structurally but assemble into different morphologies. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a 'fullerene cone' model, in which hexamers of the capsid protein are linked to form a hexagonal surface lattice that is closed by incorporating 12 capsid-protein pentamers. HIV-1 capsid protein contains an amino-terminal domain (NTD) comprising seven alpha-helices and a beta-hairpin, a carboxy-terminal domain (CTD) comprising four alpha-helices, and a flexible linker with a 310-helix connecting the two structural domains. Structures of the capsid-protein assembly units have been determined by X-ray crystallography; however, structural information regarding the assembled capsid and the contacts between the assembly units is incomplete. Here we report the cryo-electron microscopy structure of a tubular HIV-1 capsid-protein assembly at 8 A resolution and the three-dimensional structure of a native HIV-1 core by cryo-electron tomography. The structure of the tubular assembly shows, at the three-fold interface, a three-helix bundle with critical hydrophobic interactions. Mutagenesis studies confirm that hydrophobic residues in the centre of the three-helix bundle are crucial for capsid assembly and stability, and for viral infectivity. The cryo-electron-microscopy structures enable modelling by large-scale molecular dynamics simulation, resulting in all-atom models for the hexamer-of-hexamer and pentamer-of-hexamer elements as well as for the entire capsid. Incorporation of pentamers results in closer trimer contacts and induces acute surface curvature. The complete atomic HIV-1 capsid model provides a platform for further studies of capsid function and for targeted pharmacological intervention.

Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics.,Zhao G, Perilla JR, Yufenyuy EL, Meng X, Chen B, Ning J, Ahn J, Gronenborn AM, Schulten K, Aiken C, Zhang P Nature. 2013 May 30;497(7451):643-6. doi: 10.1038/nature12162. PMID:23719463<ref>PMID:23719463</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 3j3y" style="background-color:#fffaf0;"></div>

==See Also==
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
== References ==
<references/>
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[[Category: HIV Capsid]]
[[Category: Human immunodeficiency virus 1]]
[[Category: Large Structures]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Perilla JR]]
[[Category: Schulten KJ]]
[[Category: Zhang P]]
[[Category: Zhao G]]