Crystal structure of cyclophilin B at 1.2 A resolution

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 

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Structural Basis of Cyclophilin B Binding by the Calnexin/Calreticulin P-domain.

Kozlov, G.Bastos-Aristizabal, S.Maattanen, P.Rosenauer, A.Zheng, F.Killikelly, A.Trempe, J.F.Thomas, D.Y.Gehring, K.

(2010) J Biol Chem 285: 35551-35557

  • DOI: https://doi.org/10.1074/jbc.M110.160101
  • Primary Citation of Related Structures:  
    3ICH, 3ICI

  • PubMed Abstract: 

    Little is known about how chaperones in the endoplasmic reticulum are organized into complexes to assist in the proper folding of secreted proteins. One notable exception is the complex of ERp57 and calnexin that functions as part the calnexin cycle to direct disulfide bond formation in N-glycoproteins. Here, we report three new complexes composed of the peptidyl prolyl cis-trans-isomerase cyclophilin B and any of the lectin chaperones: calnexin, calreticulin, or calmegin. The 1.7 Å crystal structure of cyclophilin with the proline-rich P-domain of calmegin reveals that binding is mediated by the same surface that binds ERp57. We used NMR titrations and mutagenesis to measure low micromolar binding of cyclophilin to all three lectin chaperones and identify essential interfacial residues. The immunosuppressant cyclosporin A did not affect complex formation, confirming the functional independence of the P-domain binding and proline isomerization sites of cyclophilin. Our results reveal the P-domain functions as a unique protein-protein interaction domain and implicate a peptidyl prolyl isomerase as a new element in the calnexin cycle.

  • Organizational Affiliation

    Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, Québec H3G 0B1, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase B188Homo sapiensMutation(s): 0 
Gene Names: PPIBCYPB
UniProt & NIH Common Fund Data Resources
Find proteins for P23284 (Homo sapiens)
Explore P23284 
Go to UniProtKB:  P23284
PHAROS:  P23284
GTEx:  ENSG00000166794 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23284
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.665α = 90
b = 64.665β = 90
c = 39.463γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Refinement description