3APS

Crystal structure of Trx4 domain of ERdj5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of an ERAD pathway mediated by the ER-resident protein disulfide reductase ERdj5.

Hagiwara, M.Maegawa, K.Suzuki, M.Ushioda, R.Araki, K.Matsumoto, Y.Hoseki, J.Nagata, K.Inaba, K.

(2011) Mol.Cell 41: 432-444

  • DOI: 10.1016/j.molcel.2011.01.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • ER-associated degradation (ERAD) is an ER quality-control process that eliminates terminally misfolded proteins. ERdj5 was recently discovered to be a key ER-resident PDI family member protein that accelerates ERAD by reducing incorrect disulfide bon ...

    ER-associated degradation (ERAD) is an ER quality-control process that eliminates terminally misfolded proteins. ERdj5 was recently discovered to be a key ER-resident PDI family member protein that accelerates ERAD by reducing incorrect disulfide bonds in misfolded glycoproteins recognized by EDEM1. We here solved the crystal structure of full-length ERdj5, thereby revealing that ERdj5 contains the N-terminal J domain and six tandem thioredoxin domains that can be divided into the N- and C-terminal clusters. Our systematic biochemical analyses indicated that two thioredoxin domains that constitute the C-terminal cluster form the highly reducing platform that interacts with EDEM1 and reduces EDEM1-recruited substrates, leading to their facilitated degradation. The pulse-chase experiment further provided direct evidence for the sequential movement of an ERAD substrate from calnexin to the downstream EDEM1-ERdj5 complex, and then to the retrotranslocation channel, probably through BiP. We present a detailed molecular view of how ERdj5 mediates ERAD in concert with EDEM1.


    Organizational Affiliation

    Department of Molecular and Cellular Biology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DnaJ homolog subfamily C member 10
A, B
122Mus musculusMutation(s): 0 
Gene Names: Dnajc10 (Erdj5, Jpdi)
EC: 1.8.4.-
Find proteins for Q9DC23 (Mus musculus)
Go to UniProtKB:  Q9DC23
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.060α = 90.00
b = 33.419β = 92.85
c = 68.343γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
SHELXmodel building
HKL-2000data reduction
SCALEPACKdata scaling
REFMACrefinement
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance