Crystal structure of human PDI bb'a' domains

Experimental Data Snapshot

  • Resolution: 2.29 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

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Human protein-disulfide isomerase is a redox-regulated chaperone activated by oxidation of domain a'

Wang, C.Yu, J.Huo, L.Wang, L.Feng, W.Wang, C.-C.

(2012) J Biol Chem 287: 1139-1149

  • DOI: https://doi.org/10.1074/jbc.M111.303149
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Protein-disulfide isomerase (PDI), with domains arranged as abb'xa'c, is a key enzyme and chaperone localized in the endoplasmic reticulum (ER) catalyzing oxidative folding and preventing misfolding/aggregation of proteins. It has been controversial whether the chaperone activity of PDI is redox-regulated, and the molecular basis is unclear. Here, we show that both the chaperone activity and the overall conformation of human PDI are redox-regulated. We further demonstrate that the conformational changes are triggered by the active site of domain a', and the minimum redox-regulated cassette is located in b'xa'. The structure of the reduced bb'xa' reveals for the first time that domain a' packs tightly with both domain b' and linker x to form one compact structural module. Oxidation of domain a' releases the compact conformation and exposes the shielded hydrophobic areas to facilitate its high chaperone activity. Thus, the study unequivocally provides mechanistic insights into the redox-regulated chaperone activity of human PDI.

  • Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein disulfide-isomerase361Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P07237 (Homo sapiens)
Explore P07237 
Go to UniProtKB:  P07237
PHAROS:  P07237
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07237
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on D1D

Download Ideal Coordinates CCD File 
B [auth A](4S,5S)-1,2-DITHIANE-4,5-DIOL
C4 H8 O2 S2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.29 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.585α = 90
b = 76.076β = 90
c = 79.656γ = 90
Software Package:
Software NamePurpose
HKL-2000data 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: 2011-11-23
    Type: Initial release
  • Version 1.1: 2013-06-26
    Changes: Database references