Cyclophilin_5 from C. elegans

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.250 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Structural and Biological Characterisation of the Gut-Associated Cyclophilin B Isoforms from Caenorhabditis Elegans

Picken, N.C.Eschenlauer, S.Taylor, P.Page, A.P.Walkinshaw, M.D.

(2002) J Mol Biol 322: 15

  • DOI: https://doi.org/10.1016/s0022-2836(02)00712-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The free-living nematode Caenorhabditis elegans expresses 18 cyclophilin isoforms, eight of which are conserved single domain forms, comprising two closely related secreted or type B forms (CYP-5 and CYP-6). Recombinant CYP-5 has been purified, crystallised and the X-ray structure solved to a resolution of 1.75A. The detailed molecular architecture most strongly resembles the structure of human cyclophilin B with conserved changes in loop structure and N and C-terminal extensions. Interestingly, the active site pocket is occupied by a molecule of dithiothreitol though this has little effect on the geometry of the active site which is similar to other cyclophilin structures. The peptidyl-prolyl isomerase activity of CYP-5 has been characterised against the substrate N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide, and gives a k(cat)/K(m) value of 3.6x10(6)M(-1)s(-1) that compares with a value of 6.3x10(6)M(-1)s(-1) for human cyclophilin B. The immunosuppressive drug cyclosporin A binds and inhibits CYP-5 with an IC(50) value of 50nM, which is comparable to the value of 84nM found for human cyclophilin B. CYP-6 has 67% sequence identity with CYP-5 and a molecular model was built based on the CYP-5 crystal structure. The model shows that CYP-5 and CYP-6 are likely to have very similar structures, but with a markedly increased number of negative charges distributed around the surface of CYP-6. The spatial expression patterns of the cyclophilin B isoforms were examined using transgenic animals carrying a LacZ reporter fusion to these genes, and both cyp-5 and cyp-6 are found to be expressed in an overlapping fashion in the nematode gut. The temporal expression pattern of cyp-5 was further determined and revealed a constitutive expression pattern, with highest abundance levels being found in the embryo.

  • Organizational Affiliation

    Structural Biochemistry Group, Institute of Cell and Molecular Biology, University of Edinburgh, Michael Swann Building, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 5182Caenorhabditis elegansMutation(s): 1 
Find proteins for P52013 (Caenorhabditis elegans)
Explore P52013 
Go to UniProtKB:  P52013
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52013
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DTT

Download Ideal Coordinates CCD File 
C4 H10 O2 S2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.250 
  • R-Value Observed: 0.182 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.115α = 90
b = 94.115β = 90
c = 41.239γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-09-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-22
    Changes: Data collection, Other, Refinement description
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description