3UEM

Crystal structure of human PDI bb'a' domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 10.1074/jbc.M111.303149
  • Primary Citation of Related Structures:  
    3UEM

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein disulfide-isomeraseA361Homo sapiensMutation(s): 0 
Gene Names: PDIP4HBERBA2LPDIA1PO4DB
EC: 5.3.4.1
Find proteins for P07237 (Homo sapiens)
Explore P07237 
Go to UniProtKB:  P07237
NIH Common Fund Data Resources
PHAROS  P07237
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D1D
Query on D1D

Download CCD File 
A
(4S,5S)-1,2-DITHIANE-4,5-DIOL
C4 H8 O2 S2
YPGMOWHXEQDBBV-QWWZWVQMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-23
    Type: Initial release
  • Version 1.1: 2013-06-26
    Changes: Database references