3EC3

Crystal structure of the bb fragment of ERp72


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the Noncatalytic Domains and Global Fold of the Protein Disulfide Isomerase ERp72.

Kozlov, G.Maattanen, P.Schrag, J.D.Hura, G.L.Gabrielli, L.Cygler, M.Thomas, D.Y.Gehring, K.

(2009) Structure 17: 651-659

  • DOI: 10.1016/j.str.2009.02.016

  • PubMed Abstract: 
  • Protein disulfide isomerases are a family of proteins that catalyze the oxidation and isomerization of disulfide bonds in newly synthesized proteins in the endoplasmic reticulum. The family includes general enzymes such as PDI that recognize unfolded ...

    Protein disulfide isomerases are a family of proteins that catalyze the oxidation and isomerization of disulfide bonds in newly synthesized proteins in the endoplasmic reticulum. The family includes general enzymes such as PDI that recognize unfolded proteins, and others that are selective for specific classes of proteins. Here, we report the X-ray crystal structure of central non-catalytic domains of a specific isomerase, ERp72 (also called CaBP2 and protein disulfide-isomerase A4) from Rattus norvegicus. The structure reveals strong similarity to ERp57, a PDI-family member that interacts with the lectin-like chaperones calnexin and calreticulin but, unexpectedly, ERp72 does not interact with calnexin as shown by isothermal titration calorimetry and nuclear magnetic resonance (NMR) spectroscopy. Small-angle X-ray scattering (SAXS) of ERp72 was used to develop models of the full-length protein using both rigid body refinement and ab initio simulated annealing of dummy atoms. The two methods show excellent agreement and define the relative positions of the five thioredoxin-like domains of ERp72 and potential substrate or chaperone binding sites.


    Organizational Affiliation

    Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montréal, Québec, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein disulfide-isomerase A4
A, B
250Rattus norvegicusGene Names: Pdia4 (Cabp2, Erp70)
EC: 5.3.4.1
Find proteins for P38659 (Rattus norvegicus)
Go to UniProtKB:  P38659
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.188 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 62.171α = 90.00
b = 62.171β = 90.00
c = 135.004γ = 120.00
Software Package:
Software NamePurpose
SHARPphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance