4DGE | pdb_00004dge

TRIMCyp cyclophilin domain from Macaca mulatta: H70C mutant, HIV-1 CA(O-loop) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.255 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 68.32 kDa 
  • Atom Count: 4,880 
  • Modeled Residue Count: 609 
  • Deposited Residue Count: 622 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TRIMCyp
A, B
165Macaca mulattaMutation(s): 1 
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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
capsid protein
C, D
146Human immunodeficiency virus 1Mutation(s): 8 
Gene Names: gag
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.255 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.07α = 65.08
b = 59.71β = 83.87
c = 70.47γ = 79.65
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

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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
  • Version 1.4: 2024-11-27
    Changes: Structure summary