9H0C | pdb_00009h0c

Crystal structure of BiP ATPase domain in complex with CDNF C-terminal domain at 1.65 angstroms resolution

• PDB DOI: https://doi.org/10.2210/pdb9H0C/pdb

• Classification: CHAPERONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-08 Released: 2025-10-29 
• Deposition Author(s): Fudo, S., Shpironok, O., Saarma, M., Kajander, T.
• Funding Organization(s): Jane and Aatos Erkko Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.203 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Molecular basis for CDNF function in BiP chaperone cycle regulation

Fudo, S., Shpironok, O., Saarma, M., Kajander, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, fluorescence resonance energy transfer, surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 49.4 kDa 
• Atom Count: 3,649 
• Modeled Residue Count: 421 
• Deposited Residue Count: 442 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmic reticulum chaperone BiP	A	381	Homo sapiens	Mutation(s): 0  Gene Names: HSPA5, GRP78 EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P11021 (Homo sapiens) Explore P11021  Go to UniProtKB:  P11021
PHAROS:  P11021 GTEx:  ENSG00000044574

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cerebral dopamine neurotrophic factor	B	61	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q49AH0 (Homo sapiens) Explore Q49AH0  Go to UniProtKB:  Q49AH0
PHAROS:  Q49AH0 GTEx:  ENSG00000185267

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.203 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.522	α = 90
b = 80.612	β = 90
c = 102.349	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Fudo, S., Shpironok, O., Saarma, M., Kajander, T.

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Funding Organization	Location	Grant Number
Jane and Aatos Erkko Foundation	Finland	--

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release