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

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Basic information

Entry
Database: PDB / ID: 9uji
TitleCrystal structure of the BTB domain mouse Keap1 in complex with CDDO-Im
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 / ubiquitin-dependent protein catabolic process / midbody / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / regulation of autophagy / protein ubiquitination / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / 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
Chem-SXJ / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.435 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-Im
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)120,75718
Polymers116,7278
Non-polymers4,03010
Water00
1
A: Kelch-like ECH-associated protein 1
B: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2095
Polymers29,1822
Non-polymers1,0273
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-42 kcal/mol
Surface area13510 Å2
MethodPISA
2
C: Kelch-like ECH-associated protein 1
D: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2095
Polymers29,1822
Non-polymers1,0273
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-41 kcal/mol
Surface area13690 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)30,1694
Polymers29,1822
Non-polymers9872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-33 kcal/mol
Surface area13080 Å2
MethodPISA
4
G: Kelch-like ECH-associated protein 1
H: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1694
Polymers29,1822
Non-polymers9872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-38 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.554, 79.464, 110.876
Angle α, β, γ (deg.)90.000, 94.602, 90.000
Int Tables number4
Space group name H-MP1211

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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-SXJ / (13alpha,18alpha)-2-cyano-3-hydroxy-12-oxooleana-2,9(11)-dien-28-oic acid


Mass: 493.677 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C31H43NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
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: 2.77 Å3/Da / Density % sol: 55.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100mM Tris-HCl (pH 8.0), 200mM CaCl2, 13% PEG 3350, 2% 2-propanol

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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: Oct 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.435→42.52 Å / Num. obs: 46884 / % possible obs: 97.79 % / Redundancy: 3.5 % / CC1/2: 0.998 / Net I/σ(I): 15.32
Reflection shellResolution: 2.435→2.48 Å / Num. unique obs: 2659 / CC1/2: 0.889

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.435→42.52 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.027 / SU ML: 0.224 / Cross valid method: FREE R-VALUE / ESU R: 0.443 / ESU R Free: 0.288
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2564 2345 5.002 %
Rwork0.2057 44539 -
all0.208 --
obs-46876 97.781 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 74.706 Å2
Baniso -1Baniso -2Baniso -3
1--3.978 Å20 Å2-0.321 Å2
2--2.056 Å20 Å2
3---1.949 Å2
Refinement stepCycle: LAST / Resolution: 2.435→42.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8078 0 282 0 8360
LS refinement shellResolution: 2.435→2.48 Å
RfactorNum. reflection% reflection
Rfree0.3411 133 -
Rwork0.2924 2659 -
obs--94.86 %

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