3BOA | pdb_00003boa

Crystal structure of yeast protein disulfide isomerase.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 
    0.340 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

The Catalytic Activity of Protein-disulfide Isomerase Requires a Conformationally Flexible Molecule.

Tian, G.Kober, F.X.Lewandrowski, U.Sickmann, A.Lennarz, W.J.Schindelin, H.

(2008) J Biological Chem 283: 33630-33640

  • DOI: https://doi.org/10.1074/jbc.M806026200
  • Primary Citation Related Structures: 
    3BOA

  • PubMed Abstract: 

    Protein-disulfide isomerase (PDI) catalyzes the formation of the correct pattern of disulfide bonds in secretory proteins. A low resolution crystal structure of yeast PDI described here reveals large scale conformational changes compared with the initially reported structure, indicating that PDI is a highly flexible molecule with its catalytic domains, a and a', representing two mobile arms connected to a more rigid core composed of the b and b' domains. Limited proteolysis revealed that the linker between the a domain and the core is more susceptible to degradation than that connecting the a' domain to the core. By restricting the two arms with inter-domain disulfide bonds, the molecular flexibility of PDI, especially that of its a domain, was demonstrated to be essential for the enzymatic activity in vitro and in vivo. The crystal structure also featured a PDI dimer, and a propensity to dimerize in solution and in the ER was confirmed by cross-linking experiments and the split green fluorescent protein system. Although sedimentation studies suggested that the self-association of PDI is weak, we hypothesize that PDI exists as an interconvertible mixture of monomers and dimers in the endoplasmic reticulum due to its high abundance in this compartment.


  • Organizational Affiliation
    • Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215, USA.

Macromolecule Content 

  • Total Structure Weight: 56.42 kDa 
  • Atom Count: 3,864 
  • Modeled Residue Count: 490 
  • Deposited Residue Count: 504 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein disulfide-isomerase504Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PDI1MFP1TRG1
EC: 5.3.4.1
UniProt
Find proteins for P17967 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17967 
Go to UniProtKB:  P17967
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17967
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free:  0.340 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.921α = 90
b = 123.154β = 90
c = 75.721γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary