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3j3q
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| - | ==== | + | ==Atomic-level structure of the entire HIV-1 capsid== |
| - | <SX load='3j3q' size='340' side='right' | + | <SX load='3j3q' size='340' side='right' viewer='molstar' caption='[[3j3q]]' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [ | + | <table><tr><td colspan='2'>[[3j3q]] is a 1356 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=1vu4 1vu4], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vu5 1vu5], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vu6 1vu6], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vu7 1vu7], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vu8 1vu8], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vu9 1vu9], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vua 1vua], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vuc 1vuc], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vud 1vud], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vue 1vue], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vuf 1vuf], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vug 1vug], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vuh 1vuh], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vui 1vui], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vuj 1vuj], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vuk 1vuk], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vul 1vul], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vum 1vum], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vun 1vun], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vuo 1vuo], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vup 1vup], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vuq 1vuq], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vur 1vur], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vus 1vus] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vut 1vut]. 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=3J3Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J3Q FirstGlance]. <br> |
| - | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | </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=3j3q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j3q OCA], [https://pdbe.org/3j3q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j3q RCSB], [https://www.ebi.ac.uk/pdbsum/3j3q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j3q ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == 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] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == 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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 3j3q" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</SX> | </SX> | ||
| - | [[Category: | + | [[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]] | ||
Current revision
Atomic-level structure of the entire HIV-1 capsid
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