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- PDB-9ujj: Crystal structure of the BTB domain mouse Keap1 in complex with C... -

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Basic information

Entry
Database: PDB / ID: 9ujj
TitleCrystal structure of the BTB domain mouse Keap1 in complex with CDDO-Me
ComponentsKelch-like ECH-associated protein 1
KeywordsTRANSCRIPTION / stress sensor
Function / homology
Function and homology information


regulation of epidermal cell differentiation / Neddylation / Ub-specific processing proteases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / transcription regulator inhibitor activity / inclusion body ...regulation of epidermal cell differentiation / Neddylation / Ub-specific processing proteases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / transcription regulator inhibitor activity / inclusion body / cellular response to interleukin-4 / actin filament / centriolar satellite / disordered domain specific binding / cellular response to oxidative stress / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / protein ubiquitination / regulation of autophagy / regulation of DNA-templated transcription / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch motif / Kelch / Kelch repeat type 1 / Kelch-type beta propeller ...Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch motif / Kelch / Kelch repeat type 1 / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
: / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.43 Å
AuthorsIso, T. / Suzuki, T. / Takagi, K. / Mizushima, T. / Yamamoto, M.
Funding support Japan, 5items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)21H05270 Japan
Japan Society for the Promotion of Science (JSPS)22K06876 Japan
Japan Society for the Promotion of Science (JSPS)25K02449 Japan
Japan Society for the Promotion of Science (JSPS)24K01968 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121038 Japan
CitationJournal: To Be Published
Title: Crystal structure of the BTB domain mouse Keap1 in complex with CDDO-Me
Authors: Suzuki, T. / Takagi, K. / Iso, T. / Wen, H. / Zhang, A. / Hatakeyama, T. / Mizushima, T. / Yamamoto, M.
History
DepositionApr 17, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kelch-like ECH-associated protein 1
B: Kelch-like ECH-associated protein 1
C: Kelch-like ECH-associated protein 1
D: Kelch-like ECH-associated protein 1
E: Kelch-like ECH-associated protein 1
F: Kelch-like ECH-associated protein 1
G: Kelch-like ECH-associated protein 1
H: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,25613
Polymers116,7278
Non-polymers2,5285
Water00
1
A: Kelch-like ECH-associated protein 1
D: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1934
Polymers29,1822
Non-polymers1,0112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-36 kcal/mol
Surface area12930 Å2
MethodPISA
2
B: Kelch-like ECH-associated protein 1
C: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6873
Polymers29,1822
Non-polymers5061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-33 kcal/mol
Surface area12720 Å2
MethodPISA
3
E: Kelch-like ECH-associated protein 1
F: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1934
Polymers29,1822
Non-polymers1,0112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-37 kcal/mol
Surface area12260 Å2
MethodPISA
4
G: Kelch-like ECH-associated protein 1

H: Kelch-like ECH-associated protein 1


Theoretical massNumber of molelcules
Total (without water)29,1822
Polymers29,1822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_446-x-1/2,y-1/2,-z+11
Buried area2870 Å2
ΔGint-29 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)324.477, 72.101, 92.679
Angle α, β, γ (deg.)90.000, 103.294, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Kelch-like ECH-associated protein 1 / Cytosolic inhibitor of Nrf2 / INrf2


Mass: 14590.904 Da / Num. of mol.: 8 / Mutation: S172A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Keap1, Inrf2, Kiaa0132 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z2X8
#2: Chemical
ChemComp-A1L9B / 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 / CDDO-Me


Mass: 505.688 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C32H43NO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.52 Å3/Da / Density % sol: 72.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100mM AAB (pH 7.0), 6% PEG 20000, 200mM Ammonium sulfate, 100mM arginine, 100mM Glutamic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.43→46.26 Å / Num. obs: 27690 / % possible obs: 96.26 % / Redundancy: 3.4 % / Biso Wilson estimate: 143.03 Å2 / CC1/2: 1 / Net I/σ(I): 16.47
Reflection shellResolution: 3.43→3.553 Å / Num. unique obs: 2672 / CC1/2: 0.956

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.43→46.26 Å / SU ML: 0.5553 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 42.2614
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.32 1374 5 %
Rwork0.2522 26106 -
obs0.2554 27480 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 195.55 Å2
Refinement stepCycle: LAST / Resolution: 3.43→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7627 0 185 0 7812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00827955
X-RAY DIFFRACTIONf_angle_d1.070210809
X-RAY DIFFRACTIONf_chiral_restr0.06511267
X-RAY DIFFRACTIONf_plane_restr0.00731354
X-RAY DIFFRACTIONf_dihedral_angle_d19.31932971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.43-3.550.57941290.52692463X-RAY DIFFRACTION92.9
3.55-3.690.50761380.41642593X-RAY DIFFRACTION97.22
3.69-3.860.43671380.33422602X-RAY DIFFRACTION97.23
3.86-4.060.36341360.312623X-RAY DIFFRACTION97.11
4.06-4.320.34151360.27652579X-RAY DIFFRACTION97.42
4.32-4.650.23651390.19892662X-RAY DIFFRACTION98.52
4.65-5.120.24521410.19762660X-RAY DIFFRACTION98.52
5.12-5.860.35311390.24082636X-RAY DIFFRACTION98.02
5.86-7.370.32491370.28092619X-RAY DIFFRACTION95.96
7.38-46.260.28741410.21342669X-RAY DIFFRACTION95.51

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