Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 18.01 kDa 
• Atom Count: 1315 
• Modelled Residue Count: 164 
• Deposited Residue Count: 165 
• Unique protein chains: 1

3K0R

Cryogenic structure of CypA mutant Arg55Lys

• PDB DOI: 10.2210/pdb3K0R/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-09-25 Released: 2009-12-08 
• Deposition Author(s): Fraser, J.S., Alber, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 0.236 
• R-Value Work: 0.177 
• R-Value Observed: 0.183 

Literature

Hidden alternative structures of proline isomerase essential for catalysis.

Fraser, J.S., Clarkson, M.W., Degnan, S.C., Erion, R., Kern, D., Alber, T.

(2009) Nature 462: 669-673

• PubMed: 19956261 
• DOI: 10.1038/nature08615
• Primary Citation of Related Structures:  
  3K0M, 3K0N, 3K0O, 3K0P, 3K0Q, 3K0R


• PubMed Abstract: 
  

A long-standing challenge is to understand at the atomic level how protein dynamics contribute to enzyme catalysis. X-ray crystallography can provide snapshots of conformational substates sampled during enzymatic reactions, while NMR relaxation methods reveal the rates of interconversion between substates and the corresponding relative populations. However, these current methods cannot simultaneously reveal the detailed atomic structures of the rare states and rationalize the finding that intrinsic motions in the free enzyme occur on a timescale similar to the catalytic turnover rate. Here we introduce dual strategies of ambient-temperature X-ray crystallographic data collection and automated electron-density sampling to structurally unravel interconverting substates of the human proline isomerase, cyclophilin A (CYPA, also known as PPIA). A conservative mutation outside the active site was designed to stabilize features of the previously hidden minor conformation. This mutation not only inverts the equilibrium between the substates, but also causes large, parallel reductions in the conformational interconversion rates and the catalytic rate. These studies introduce crystallographic approaches to define functional minor protein conformations and, in combination with NMR analysis of the enzyme dynamics in solution, show how collective motions directly contribute to the catalytic power of an enzyme.

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Organizational Affiliation: 

Department of Molecular and Cell Biology/QB3, University of California, Berkeley, California 94720-3220, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclophilin A	A	165	Homo sapiens	Mutation(s): 1  Gene Names: PPIA, CYPA EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62937 (Homo sapiens) Explore P62937  Go to UniProtKB:  P62937
PHAROS:  P62937 GTEx:  ENSG00000196262

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 0.236 
• R-Value Work: 0.177 
• R-Value Observed: 0.183 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.211	α = 90
b = 64.211	β = 90
c = 93.566	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-09-25 
• Released Date: 2009-12-08 
Deposition Author(s): Fraser, J.S., Alber, T.

Revision History  

• Version 1.0: 2009-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-10-10
  Changes: Data collection, Database references, Structure summary
• Version 1.4: 2021-10-13
  Changes: Database references, Structure summary