3J3Y
Atomic-level structure of the entire HIV-1 capsid (186 hexamers + 12 pentamers)
This is a non-PDB format compatible entry.
Summary for 3J3Y
| Entry DOI | 10.2210/pdb3j3y/pdb |
| Related | 3J34 3J3Q |
| EMDB information | 5639 |
| Descriptor | capsid protein (1 entity in total) |
| Functional Keywords | hiv-1 capsid, core, all-atom model, complete capsid, virus |
| Biological source | Human immunodeficiency virus 1 (HIV-1) |
| Total number of polymer chains | 1176 |
| Total formula weight | 30226128.24 |
| Authors | Perilla, J.R.,Zhao, G.,Zhang, P.,Schulten, K.J. (deposition date: 2013-05-06, release date: 2013-05-29, Last modification date: 2024-11-06) |
| Primary citation | Zhao, G.,Perilla, J.R.,Yufenyuy, E.L.,Meng, X.,Chen, B.,Ning, J.,Ahn, J.,Gronenborn, A.M.,Schulten, K.,Aiken, C.,Zhang, P. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature, 497:643-646, 2013 Cited by PubMed Abstract: 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 α-helices and a β-hairpin, a carboxy-terminal domain (CTD) comprising four α-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 Å 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. PubMed: 23719463DOI: 10.1038/nature12162 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY |
Structure validation
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