6SKM

Structure of the native full-length HIV-1 capsid protein A92E in helical assembly (-13,12)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6SLU


Literature

Intrinsic curvature of the HIV-1 CA hexamer underlies capsid topology and interaction with cyclophilin A.

Ni, T.Gerard, S.Zhao, G.Dent, K.Ning, J.Zhou, J.Shi, J.Anderson-Daniels, J.Li, W.Jang, S.Engelman, A.N.Aiken, C.Zhang, P.

(2020) Nat Struct Mol Biol 27: 855-862

  • DOI: https://doi.org/10.1038/s41594-020-0467-8
  • Primary Citation of Related Structures:  
    6SKK, 6SKM, 6SKN, 6SLQ, 6SLU, 6SMU, 6Y9V, 6Y9W, 6Y9X, 6Y9Y, 6Y9Z, 6YJ5, 6ZDJ

  • PubMed Abstract: 

    The mature retrovirus capsid consists of a variably curved lattice of capsid protein (CA) hexamers and pentamers. High-resolution structures of the curved assembly, or in complex with host factors, have not been available. By devising cryo-EM methodologies for exceedingly flexible and pleomorphic assemblies, we have determined cryo-EM structures of apo-CA hexamers and in complex with cyclophilin A (CypA) at near-atomic resolutions. The CA hexamers are intrinsically curved, flexible and asymmetric, revealing the capsomere and not the previously touted dimer or trimer interfaces as the key contributor to capsid curvature. CypA recognizes specific geometries of the curved lattice, simultaneously interacting with three CA protomers from adjacent hexamers via two noncanonical interfaces, thus stabilizing the capsid. By determining multiple structures from various helical symmetries, we further revealed the essential plasticity of the CA molecule, which allows formation of continuously curved conical capsids and the mechanism of capsid pattern sensing by CypA.


  • Organizational Affiliation

    Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gag protein
A, B, C, D, E
A, B, C, D, E, F
231Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: gag
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION2.0; 3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom206422/Z/17/Z
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP50AI150481

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2021-02-10
    Changes: Database references
  • Version 1.2: 2022-03-30
    Changes: Author supporting evidence, Database references