Biological Assembly 1  

 3D View: Structure | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 42-mer - A42 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1079.50 kDa 
• Atom Count: 75600 
• Modelled Residue Count: 9702 
• Deposited Residue Count: 9702 
• Unique protein chains: 1

3J34

Structure of HIV-1 Capsid Protein by Cryo-EM

• DOI: 10.2210/pdb3J34/pdb
• EMDataResource: EMD-5582

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-02-23 Released: 2013-05-29 
• Deposition Author(s): Zhao, G., Perilla, J.R., Yufenyuy, E., Meng, X., Chen, B., Ning, J., Ahn, J., Gronenborn, A.M., Schulten, K., Aiken, C., Zhang, P.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 8.60 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

Literature

Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics.

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.

(2013) Nature 497: 643-646

• PubMed: 23719463 
• DOI: 10.1038/nature12162
• Primary Citation of Related Structures:  
  3J34, 3J3Q, 3J3Y, 3J4F


• 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.

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Organizational Affiliation: 

Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
capsid protein	AA [auth 5], EA [auth 6], KA [auth 7], A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, BA [auth a], CA [auth b], DA [auth c], LA [auth d], MA [auth e], NA [auth f], OA [auth g], PA [auth h], FA [auth i], GA [auth j], HA [auth k], IA [auth l], JA [auth m]	231	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: gag
UniProt
Find proteins for Q79791 (Human immunodeficiency virus 1) Explore Q79791  Go to UniProtKB:  Q79791

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 8.60 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-23 
• Released Date: 2013-05-29 
Deposition Author(s): Zhao, G., Perilla, J.R., Yufenyuy, E., Meng, X., Chen, B., Ning, J., Ahn, J., Gronenborn, A.M., Schulten, K., Aiken, C., Zhang, P.

Revision History  

• Version 1.0: 2013-05-29
  Type: Initial release
  
• Version 1.1: 2013-06-12
  Changes: Database references
• Version 1.2: 2013-06-19
  Changes: Refinement description
• Version 1.3: 2018-07-18
  Changes: Author supporting evidence, Data collection