9WQU | pdb_00009wqu

b-b' domain fragment of ER-60 (ERp57) under microgravity

• PDB DOI: https://doi.org/10.2210/pdb9WQU/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-09-11 Released: 2025-10-01 
• Deposition Author(s): Furubayashi, N., Shinohara, Y., Inaka, K., Kaito, S., Kobayashi, Y., Kamo, M., Urade, R.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.263 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of b-b' domain fragment of ER-60 (ERp57) under microgravity

Furubayashi, N., Shinohara, Y., Inaka, K., Kaito, S., Kobayashi, Y., Kamo, M., Urade, R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 85.94 kDa 
• Atom Count: 6,220 
• Modeled Residue Count: 699 
• Deposited Residue Count: 756 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein disulfide-isomerase A3	A, B, C	252	Homo sapiens	Mutation(s): 0  Gene Names: PDIA3, ERP57, ERP60, GRP58 EC: 5.3.4.1
UniProt & NIH Common Fund Data Resources
Find proteins for P30101 (Homo sapiens) Explore P30101  Go to UniProtKB:  P30101
PHAROS:  P30101 GTEx:  ENSG00000167004

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.263 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.315	α = 90
b = 62.901	β = 98.64
c = 97.148	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Furubayashi, N., Shinohara, Y., Inaka, K., Kaito, S., Kobayashi, Y., Kamo, M., Urade, R.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18380079
Japan Society for the Promotion of Science (JSPS)	Japan	21380081
Japan Society for the Promotion of Science (JSPS)	Japan	25292070

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release