4DGA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/nsmb.2253
  • Primary Citation of Related Structures:  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 betw ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRIMCyp
A, B
165Macaca mulattaGene Names: PPIA (CYPA)
EC: 5.2.1.8
Find proteins for P62940 (Macaca mulatta)
Go to Gene View: PPIA
Go to UniProtKB:  P62940
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
capsid protein
C, D
146Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P12497
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 38.590α = 90.00
b = 111.350β = 102.39
c = 67.760γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
PXSOFTdata collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-03-28
    Type: Database references
  • Version 1.2: 2012-04-18
    Type: Database references