Crystal structure of oxidized hPDI (abb'xa')

Experimental Data Snapshot

  • Resolution: 2.88 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.262 

Starting Model: experimental
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Structural insights into the redox-regulated dynamic conformations of human protein disulfide isomerase

Wang, C.Li, W.Ren, J.Fang, J.Ke, H.Gong, W.Feng, W.Wang, C.-C.

(2013) Antioxid Redox Signal 19: 44-53

  • DOI: https://doi.org/10.1089/ars.2012.4630
  • Primary Citation of Related Structures:  
    4EKZ, 4EL1

  • PubMed Abstract: 

    Human protein disulfide isomerase (hPDI) is a key enzyme and a redox-regulated chaperone responsible for oxidative protein folding in the endoplasmic reticulum. This work aims to reveal the molecular mechanism underlying the redox-regulated functions of hPDI by determining the crystal structures of hPDI in different redox states. The structures of hPDI (abb'xa') in both the reduced and oxidized states showed that the four thioredoxin domains of a, b, b', and a' are arranged as a horseshoe shape with two CGHC active sites, respectively, in domains a and a' facing each other at the two ends. In reduced hPDI, domains a, b, and b' line up in the same plane, whereas domain a' twists ∼45° out. The two active sites are 27.6 Å apart. In oxidized hPDI, the four domains are differently organized to stay in the same plane, and the distance between the active sites increases to 40.3 Å. In contrast to the closed conformation of reduced hPDI, oxidized hPDI exists in an open state with more exposed hydrophobic areas and a larger cleft with potential for substrate binding. This is the first report of the high-resolution structures of hPDI containing all four domains in both the reduced and the oxidized states. It reveals the redox-regulated structural dynamic properties of the protein. The redox-regulated open/closed conformational switch of hPDI endows the protein with versatile target-binding capacities for its enzymatic and chaperone functions.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein disulfide-isomerase
A, B
482Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P07237 (Homo sapiens)
Explore P07237 
Go to UniProtKB:  P07237
GTEx:  ENSG00000185624 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07237
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.88 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.262 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.748α = 90
b = 34.014β = 104.89
c = 156.959γ = 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: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-07-03
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description