4DGC

TRIMCyp cyclophilin domain from Macaca mulatta: cyclosporin A complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRIMCyp ABCDE165Macaca mulattaMutation(s): 0 
Gene Names: TRIMCypPPIACYPA
EC: 5.2.1.8
Find proteins for P62940 (Macaca mulatta)
Explore P62940 
Go to UniProtKB:  P62940
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
cyclosporin A FGHIJ11Tolypocladium inflatumMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
F,G,H,I,JL-PEPTIDE LINKINGC4 H9 N O2ALA
BMT
Query on BMT
F,G,H,I,JL-PEPTIDE LINKINGC10 H19 N O3THR
MLE
Query on MLE
F,G,H,I,JL-PEPTIDE LINKINGC7 H15 N O2LEU
MVA
Query on MVA
F,G,H,I,JL-PEPTIDE LINKINGC6 H13 N O2VAL
SAR
Query on SAR
F,G,H,I,JPEPTIDE LINKINGC3 H7 N O2GLY
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000142
Query on PRD_000142
F, G, H, I, JCyclosporin ACyclic peptide /  Immunosuppressant

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.47α = 90
b = 108.47β = 90
c = 423.06γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PXSOFTdata collection
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: 2013-02-27
    Changes: Other