9UJJ | pdb_00009ujj

Crystal structure of the BTB domain mouse Keap1 in complex with CDDO-Me

• PDB DOI: https://doi.org/10.2210/pdb9UJJ/pdb

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


• Deposited: 2025-04-17 Released: 2025-10-22 
• Deposition Author(s): Iso, T., Suzuki, T., Takagi, K., Mizushima, T., Yamamoto, M.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.43 Å
• R-Value Free: 
  0.320 (Depositor), 0.317 (DCC) 
• R-Value Work: 
  0.252 (Depositor), 0.253 (DCC) 
• R-Value Observed: 
  0.255 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the BTB domain mouse Keap1 in complex with CDDO-Me

Suzuki, T., Takagi, K., Iso, T., Wen, H., Zhang, A., Hatakeyama, T., Mizushima, T., Yamamoto, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 119.26 kDa 
• Atom Count: 7,812 
• Modeled Residue Count: 976 
• Deposited Residue Count: 1,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch-like ECH-associated protein 1	A, B, C, D, E, F, G, H	130	Mus musculus	Mutation(s): 1  Gene Names: Keap1, Inrf2, Kiaa0132
UniProt
Find proteins for Q9Z2X8 (Mus musculus) Explore Q9Z2X8  Go to UniProtKB:  Q9Z2X8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L9B (Subject of Investigation/LOI)	I [auth A], J [auth B], K [auth D], L [auth E], M [auth F]	methyl (4aS,6aR,6bS,8aR,12aS,14aR,14bS)-11-cyano-2,2,6a,6b,9,9,12a-heptamethyl-10,14-bis(oxidanylidene)-1,3,4,5,6,7,8,8a,14a,14b-decahydropicene-4a-carboxylate C32 H43 N O4 WPTTVJLTNAWYAO-UFHYVYMVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.43 Å
• R-Value Free:  0.320 (Depositor), 0.317 (DCC) 
• R-Value Work:  0.252 (Depositor), 0.253 (DCC) 
• R-Value Observed: 0.255 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 324.477	α = 90
b = 72.101	β = 103.294
c = 92.679	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Iso, T., Suzuki, T., Takagi, K., Mizushima, T., Yamamoto, M.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	21H05270
Japan Society for the Promotion of Science (JSPS)	Japan	22K06876
Japan Society for the Promotion of Science (JSPS)	Japan	25K02449
Japan Society for the Promotion of Science (JSPS)	Japan	24K01968
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121038

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release