6YJ5

Focused refinement cryo-EM structure of the yeast mitochondrial complex I sub-stoichiometric sulfur transferase subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


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
Rhodanese-like domain-containing proteinA [auth q]315Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_128700YALI1_F30877g
UniProt
Find proteins for Q6C0L9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6C0L9 
Go to UniProtKB:  Q6C0L9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6C0L9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.14
MODEL REFINEMENTPHENIX1.16
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_U105663141
Medical Research Council (MRC, United Kingdom)United KingdomMC_UU_00015/2

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references
  • Version 1.2: 2020-10-21
    Changes: Database references
  • Version 1.3: 2021-02-10
    Changes: Database references
  • Version 1.4: 2024-05-22
    Changes: Data collection, Database references, Refinement description