5AYK | pdb_00005ayk

Crystal structure of ERdj5 form I

• PDB DOI: https://doi.org/10.2210/pdb5AYK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-08-22 Released: 2017-02-15 
• Deposition Author(s): Watanabe, S., Maegawa, K., Inaba, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.243 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Highly dynamic nature of ERdj5 is essential for enhancement of the ER associated degradation

Maegawa, K., Watanabe, S., Okumura, M., Noi, K., Inoue, M., Ushioda, R., Ogura, T., Nagata, K., Inaba, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 89.55 kDa 
• Atom Count: 6,061 
• Modeled Residue Count: 744 
• Deposited Residue Count: 783 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DnaJ homolog subfamily C member 10	A	783	Mus musculus	Mutation(s): 10  Gene Names: Dnajc10, Erdj5, Jpdi EC: 1.8.4 (PDB Primary Data), 1.8.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9DC23 (Mus musculus) Explore Q9DC23  Go to UniProtKB:  Q9DC23
IMPC:  MGI:1914111

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PS	B [auth A]	3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE C8 H11 N O3 S REEBJQTUIJTGAL-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.243 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.99	α = 90
b = 52.97	β = 113.54
c = 92.9	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-15 
Deposition Author(s): Watanabe, S., Maegawa, K., Inaba, K.

Revision History  

• Version 1.0: 2017-02-15
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-10-16
  Changes: Structure summary