1JZD | pdb_00001jzd

DsbC-DsbDalpha complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.293 (Depositor), 0.295 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.235 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

The Disulfide Bond Isomerase DsbC is Activated by an Immunoglobulin-fold Thiol Oxidoreductase: Crystal structure of the DsbC-DsbDalpha complex.

Haebel, P.W.Goldstone, D.Katzen, F.Beckwith, J.Metcalf, P.

(2002) EMBO J 21: 4774-4784

  • DOI: https://doi.org/10.1093/emboj/cdf489
  • Primary Citation Related Structures: 
    1JPE, 1JZD, 1JZO

  • PubMed Abstract: 

    The Escherichia coli disulfide bond isomerase DsbC rearranges incorrect disulfide bonds during oxidative protein folding. It is specifically activated by the periplasmic N-terminal domain (DsbDalpha) of the transmembrane electron transporter DsbD. An intermediate of the electron transport reaction was trapped, yielding a covalent DsbC-DsbDalpha complex. The 2.3 A crystal structure of the complex shows for the first time the specific interactions between two thiol oxidoreductases. DsbDalpha is a novel thiol oxidoreductase with the active site cysteines embedded in an immunoglobulin fold. It binds into the central cleft of the V-shaped DsbC dimer, which assumes a closed conformation on complex formation. Comparison of the complex with oxidized DsbDalpha reveals major conformational changes in a cap structure that regulates the accessibility of the DsbDalpha active site. Our results explain how DsbC is selectively activated by DsbD using electrons derived from the cytoplasm.


  • Organizational Affiliation
    • School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealandand.

Macromolecule Content 

  • Total Structure Weight: 62.38 kDa 
  • Atom Count: 4,347 
  • Modeled Residue Count: 551 
  • Deposited Residue Count: 572 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
thiol:disulfide interchange protein dsbc
A, B
220Escherichia coliMutation(s): 1 
Gene Names: dsbC
UniProt
Find proteins for P0AEG6 (Escherichia coli (strain K12))
Explore P0AEG6 
Go to UniProtKB:  P0AEG6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEG6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
thiol:disulfide interchange protein dsbd132Escherichia coliMutation(s): 1 
Gene Names: dsbD
EC: 1.8.1.8
UniProt
Find proteins for P36655 (Escherichia coli (strain K12))
Explore P36655 
Go to UniProtKB:  P36655
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36655
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.293 (Depositor), 0.295 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.235 (DCC) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.91α = 90
b = 68.91β = 90
c = 230.336γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Data collection, Database references
  • Version 1.4: 2023-08-16
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-11-20
    Changes: Structure summary