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
  • Structures With Same Primary Citation

  • 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, C, D, E
165Macaca mulattaMutation(s): 0 
Gene Names: TRIMCyp
EC: 5.2.1.8
Find proteins for B0LJC8 (Macaca mulatta)
Go to UniProtKB:  B0LJC8
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
cyclosporin A
F, G, H, I, J
11Tolypocladium inflatumMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000142
Query on PRD_000142
F, G, H, I, JCyclosporin ACyclic peptide /  Immunosuppressant

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Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
F,G,H,I,J
L-PEPTIDE LINKINGC4 H9 N O2ALA
BMT
Query on BMT
F,G,H,I,J
L-PEPTIDE LINKINGC10 H19 N O3THR
MLE
Query on MLE
F,G,H,I,J
L-PEPTIDE LINKINGC7 H15 N O2LEU
MVA
Query on MVA
F,G,H,I,J
L-PEPTIDE LINKINGC6 H13 N O2VAL
SAR
Query on SAR
F,G,H,I,J
PEPTIDE LINKINGC3 H7 N O2GLY
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 

  • 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