3ICI

Crystal structure of cyclophilin B in complex with calmegin fragment

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

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: 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 ...

    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.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase B A, B188Homo sapiensMutation(s): 0 
Gene Names: PPIB, CYPB
EC: 5.2.1.8
Find proteins for P23284 (Homo sapiens)
Explore P23284 
Go to UniProtKB:  P23284
NIH Common Fund Data Resources
PHAROS:  P23284
GTEx:  ENSG00000166794
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Calnexin C38Canis lupus familiarisMutation(s): 0 
Gene Names: CANX, CLGN
Find proteins for E2RA18 (Canis lupus familiaris)
Explore E2RA18 
Go to UniProtKB:  E2RA18
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES
Download Ideal Coordinates CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.411α = 89.94
b = 44.295β = 94.46
c = 55.427γ = 114.03
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
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