2B5E | pdb_00002b5e

Crystal Structure of Yeast Protein Disulfide Isomerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.246 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.191 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

The crystal structure of yeast protein disulfide isomerase suggests cooperativity between its active sites.

Tian, G.Xiang, S.Noiva, R.Lennarz, W.J.Schindelin, H.

(2006) Cell 124: 61-73

  • DOI: https://doi.org/10.1016/j.cell.2005.10.044
  • Primary Citation Related Structures: 
    2B5E

  • PubMed Abstract: 

    Protein disulfide isomerase plays a key role in catalyzing the folding of secretory proteins. It features two catalytically inactive thioredoxin domains inserted between two catalytically active thioredoxin domains and an acidic C-terminal tail. The crystal structure of yeast PDI reveals that the four thioredoxin domains are arranged in the shape of a twisted "U" with the active sites facing each other across the long sides of the "U." The inside surface of the "U" is enriched in hydrophobic residues, thereby facilitating interactions with misfolded proteins. The domain arrangement, active site location, and surface features strikingly resemble the Escherichia coli DsbC and DsbG protein disulfide isomerases. Biochemical studies demonstrate that all domains of PDI, including the C-terminal tail, are required for full catalytic activity. The structure defines a framework for rationalizing the differences between the two active sites and their respective roles in catalyzing the formation and rearrangement of disulfide bonds.


  • Organizational Affiliation
    • Department of Biochemistry and Cell Biology, State University of New York at Stony Brook, NY 11794, USA.

Macromolecule Content 

  • Total Structure Weight: 56.74 kDa 
  • Atom Count: 3,975 
  • Modeled Residue Count: 483 
  • 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: 2.40 Å
  • R-Value Free:  0.246 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.191 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.56α = 90
b = 136.56β = 90
c = 69.524γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary