4FRU

Crystal structure of horse wild-type cyclophilin B

• PDB DOI: https://doi.org/10.2210/pdb4FRU/pdb

• Classification: ISOMERASE
• Organism(s): Equus caballus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-06-26 Released: 2012-11-14 
• Deposition Author(s): Boudko, S.P., Ishikawa, Y., Bachinger, H.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.139 
• R-Value Work: 0.116 
• R-Value Observed: 0.117 

Starting Model: experimental

Literature

Crystal structures of wild-type and mutated cyclophilin B that causes hyperelastosis cutis in the American quarter horse.

Boudko, S.P., Ishikawa, Y., Lerch, T.F., Nix, J., Chapman, M.S., Bachinger, H.P.

(2012) BMC Res Notes 5: 626-626

• PubMed: 23137129 
• DOI: https://doi.org/10.1186/1756-0500-5-626
• Primary Citation of Related Structures:  
  4FRU, 4FRV


• PubMed Abstract: 
  

  Hyperelastosis cutis is an inherited autosomal recessive connective tissue disorder. Affected horses are characterized by hyperextensible skin, scarring, and severe lesions along the back. The disorder is caused by a mutation in cyclophilin B. The crystal structures of both wild-type and mutated (Gly6->Arg) horse cyclophilin B are presented. The mutation neither affects the overall fold of the enzyme nor impairs the catalytic site structure. Instead, it locally rearranges the flexible N-terminal end of the polypeptide chain and also makes it more rigid. Interactions of the mutated cyclophilin B with a set of endoplasmic reticulum-resident proteins must be affected.

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Organizational Affiliation: 

Research Department, Shriners Hospital for Children, Portland, OR 97239, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20.85 kDa 
• Atom Count: 1,772 
• Modelled Residue Count: 185 
• Deposited Residue Count: 185 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase	A	185	Equus caballus	Mutation(s): 0  Gene Names: PPIB EC: 5.2.1.8
UniProt
Find proteins for A5YBL8 (Equus caballus) Explore A5YBL8  Go to UniProtKB:  A5YBL8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ME2	D [auth A]	1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE C7 H16 O3 CNJRPYFBORAQAU-UHFFFAOYSA-N
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.139 
• R-Value Work: 0.116 
• R-Value Observed: 0.117 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.88	α = 90
b = 44.07	β = 95.2
c = 60.57	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Boudko, S.P., Ishikawa, Y., Bachinger, H.P.

Revision History  

• Version 1.0: 2012-11-14
  Type: Initial release
  
• Version 1.1: 2013-01-09
  Changes: Database references
• Version 1.2: 2013-03-13
  Changes: Refinement description
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description