4DGB

TRIMCyp cyclophilin domain from Macaca mulatta: HIV-2 CA cyclophilin-binding loop complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Diverse HIV viruses are targeted by a conformationally dynamic antiviral.

Caines, M.E.Bichel, K.Price, A.J.McEwan, W.A.Towers, G.J.Willett, B.J.Freund, S.M.James, L.C.

(2012) Nat Struct Mol Biol 19: 411-416

  • DOI: https://doi.org/10.1038/nsmb.2253
  • Primary Citation of Related Structures:  
    4DGA, 4DGB, 4DGC, 4DGD, 4DGE

  • PubMed Abstract: 

    Rhesus macaque TRIMCyp (RhTC) is a potent primate antiviral host protein that inhibits the replication of diverse HIV viruses. Here we show that it has acquired the ability to target multiple viruses by evolving an active site that interconverts between multiple conformations. Mutations that have relieved active site constraints allow RhTC to dynamically sample conformational space, including radically different conformers that target both HIV-1 and HIV-2 viruses. Introduction of a reversible constraint into RhTC allows specificity to be switched between a single conformation specific for HIV-1 and a dynamic ensemble that targets multiple viruses. These results show that conformational diversity can be used to expand the target diversity of innate immune receptors by supplementing their limited genetic variability with variability in protein structure.


  • Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Division of Protein and Nucleic Acid Chemistry, Cambridge, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRIMCyp165Macaca mulattaMutation(s): 0 
Gene Names: TRIMCyp
EC: 5.2.1.8
UniProt
Find proteins for P62940 (Macaca mulatta)
Explore P62940 
Go to UniProtKB:  P62940
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62940
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
capsid protein6Human immunodeficiency virus type 2 (ISOLATE ROD)Mutation(s): 0 
UniProt
Find proteins for P04590 (Human immunodeficiency virus type 2 subtype A (isolate ROD))
Explore P04590 
Go to UniProtKB:  P04590
Entity Groups  
UniProt GroupP04590
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.17α = 90
b = 55.72β = 90
c = 70.84γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-03-28
    Changes: Database references
  • Version 1.2: 2012-04-18
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Refinement description