Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18.57 kDa 
• Atom Count: 1522 
• Modelled Residue Count: 169 
• Deposited Residue Count: 171 
• Unique protein chains: 2

4DGB

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

• DOI: 10.2210/pdb4DGB/pdb

• Classification: ISOMERASE/VIRAL PROTEIN
• Organism(s): Macaca mulatta, Human immunodeficiency virus type 2 (ISOLATE ROD)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-25 Released: 2012-02-08 
• Deposition Author(s): Caines, M.E.C., Bichel, K., Price, A.J., McEwan, W.A., James, L.C.

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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 

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

• PubMed: 22407016 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRIMCyp	A	165	Macaca mulatta	Mutation(s): 0  Gene Names: TRIMCyp, PPIA, CYPA EC: 5.2.1.8
Find proteins for P62940 (Macaca mulatta) Explore P62940  Go to UniProtKB:  P62940

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
capsid protein	B	6	Human immunodeficiency virus type 2 (ISOLATE ROD)	Mutation(s): 0  Gene Names: gag
Find proteins for P04590 (Human immunodeficiency virus type 2 subtype A (isolate ROD)) Explore P04590  Go to UniProtKB:  P04590

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 = 36.17	α = 90
b = 55.72	β = 90
c = 70.84	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-25 
• Released Date: 2012-02-08 
Deposition Author(s): Caines, M.E.C., Bichel, K., Price, A.J., McEwan, W.A., James, L.C.

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