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)

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Bidirectional regulation of KEAP1 BTB domain-based sensor activity.

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

(2025) Redox Biol 87: 103885-103885

PubMed: 41092551 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.redox.2025.103885
Primary Citation Related Structures:
9UJG, 9UJI, 9UJJ

PubMed Abstract:
The KEAP1-CUL3 ubiquitin ligase regulates protein stability of transcriptional factor NRF2 and plays critical roles in cellular stress response. The BTB domain of KEAP1 functions as a sensor for electrophilic chemicals. However, the precise mechanisms by which electrophiles are recognized and inhibit BTB activity remain unclear. Here, we show that electrophilic modification alters the spatial arrangement of the BTB homodimer, regulating its ligase activity. Co-crystal structural analyses and functional studies using potent NRF2-inducing CDDO-derivatives, synthetic electrophilic compounds structurally related to clinically approved molecules such as Omaveloxolone, revealed that the key sensor residue, Cys151, resides in a structurally elaborate environment within the BTB domain. Modification of Cys151 by NRF2 inducers changes the spatial configuration of the CUL3-binding sites in the BTB homodimer, reducing KEAP1-CUL3 complex affinity. In contrast, a Cys151-targeting NRF2 inhibitor induces an opposite rearrangement of the BTB homodimer. This study elucidates the molecular mechanism by which the BTB domain finely regulates KEAP1-CUL3 ubiquitin ligase activity.

Organizational Affiliation

Department of Biochemistry & Molecular Biology, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan; Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan. Electronic address: takafumi.suzuki.d5@tohoku.ac.jp.

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

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch-like ECH-associated protein 1	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Z2X8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L9B (Subject of Investigation/LOI) Query on A1L9B Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth D] SDF format, chain L [auth E] SDF format, chain M [auth F] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth D] MOL2 format, chain L [auth E] MOL2 format, chain M [auth F] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth D] mmCIF format, chain L [auth E] mmCIF format, chain M [auth F]	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		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth F] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth F]

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

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