Biological Assembly 1  

 3D View: Structure

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 
• 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
• Structures With Same Primary Citation


• 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
capsid protein	5, 6, 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, a, b, c, d, e, f, g, h, i, j, k, l, m	231	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: gag
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