3APO

Crystal structure of full-length ERdj5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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:  
    3APS, 3APO, 3APQ

  • 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 bonds in misfolded glycoproteins recognized by EDEM1 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DnaJ homolog subfamily C member 10A780Mus musculusMutation(s): 11 
Gene Names: Dnajc10Erdj5Jpdi
EC: 1.8.4
Find proteins for Q9DC23 (Mus musculus)
Explore Q9DC23 
Go to UniProtKB:  Q9DC23
NIH Common Fund Data Resources
IMPC:  MGI:1914111
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.1α = 90
b = 53.4β = 113.4
c = 92.3γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHELXmodel building
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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