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- PDB-9vd2: Crystal Structure of kelch domain of human KEAP1 in complex with ... -

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Entry
Database: PDB / ID: 9vd2
TitleCrystal Structure of kelch domain of human KEAP1 in complex with CH7286675
ComponentsKelch-like ECH-associated protein 1
KeywordsTRANSCRIPTION / BETA-PROPELLER / KELCH REPEAT MOTIF / PROTEIN BINDIN
Function / homology
Function and homology information


regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / 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 ...regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / 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 / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / midbody / in utero embryonic development / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / Ub-specific processing proteases / regulation of autophagy / protein ubiquitination / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Kelch-like ECH-associated protein 1 / : / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch motif / Kelch / Kelch repeat type 1 ...Kelch-like ECH-associated protein 1 / : / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / 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
: / ACETATE ION / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 Å
AuthorsKawauchi, H. / Fukami, T.A. / Kimbara, A. / Miyagi, T. / Yasui, Y. / Hoshino, M. / Irie, M. / Torizawa, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of kelch domain of human KEAP1 in complex with CH7286675
Authors: Kawauchi, H.
History
DepositionJun 7, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 15, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,41914
Polymers31,9521
Non-polymers1,46713
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-0 kcal/mol
Surface area11740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.642, 76.41, 48.222
Angle α, β, γ (deg.)90, 105.44, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Kelch-like ECH-associated protein 1 / Cytosolic inhibitor of Nrf2 / INrf2 / Kelch-like protein 19


Mass: 31951.773 Da / Num. of mol.: 1 / Mutation: E540A/E542A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145
#2: Chemical ChemComp-A1L99 / 4-[3-[2,6-dichloro-4-(6-methoxy-2-azaspiro[3.3]heptan-2-yl)benzoyl]-2,4-dihydro-1,3-benzoxazin-8-yl]-5-fluoro-2-(3-oxa-8-azabicyclo[3.2.1]octan-8-yl)benzoic acid


Mass: 682.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H34Cl2FN3O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
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: 3.52 Å3/Da / Density % sol: 65.05 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 3.14M Ammonium acetate, 17.6% v/v Dimethyl sulfoxide, 0.1M Tris (pH 8.5)

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.02 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.699→64.768 Å / Num. obs: 38151 / % possible obs: 93 % / Redundancy: 7.05 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.99 / CC1/2 anomalous: -0.061 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.0805 / Rrim(I) all: 0.215 / AbsDiff over sigma anomalous: 0.744 / Baniso tensor eigenvalue 1: 0.5838 Å2 / Baniso tensor eigenvalue 2: 0 Å2 / Baniso tensor eigenvalue 3: 11.6458 Å2 / Baniso tensor eigenvector 1 ortho1: 0.7835 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: -0.6214 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0.6214 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 0.7835 / Aniso diffraction limit 1: 2.048 Å / Aniso diffraction limit 2: 1.708 Å / Aniso diffraction limit 3: 1.668 Å / Aniso diffraction limit axis 1 ortho1: 0.73433 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0.67882 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: -0.67882 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 0.73433 / Net I/σ(I): 7.72 / Num. measured all: 268917 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 92.6 / % possible ellipsoidal: 93 / % possible ellipsoidal anomalous: 92.6 / % possible spherical: 78.1 / % possible spherical anomalous: 77.7 / Redundancy anomalous: 3.59 / Signal type: local
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
5.066-64.7687.290.065222.621391013910190819080.959-0.1970.02660.07060.75999.910099.910099.93.83100
4.006-5.0667.570.058524.381443414434190719070.997-0.180.02280.06280.7131001001001001003.89100
3.494-4.0057.590.077819.931448514485190819080.996-0.1220.03030.08350.7431001001001001003.89100
3.17-3.4937.240.101115.651380113801190719070.993-0.1630.04020.10890.74999.910099.910099.93.7100
2.941-3.176.140.136211.211172411724190819080.987-0.0860.05960.1490.761001001001001003.14100
2.766-2.946.320.16819.661204312043190719070.98-0.0090.07270.18350.78799.910099.910099.93.22100
2.625-2.7666.810.23137.531298812988190819080.9750.0140.09550.25060.8061001001001001003.47100
2.511-2.62570.28886.221334913349190719070.9670.0210.11740.31210.77399.910099.910099.93.57100
2.413-2.5117.10.37165.111355313553190819080.938-0.0530.14990.40110.7391001001001001003.61100
2.329-2.4137.140.394.931361513615190819080.942-0.0440.1570.42080.7531001001001001003.63100
2.255-2.3297.210.4474.371374913749190719070.9330.0150.17910.4820.74799.910099.910099.93.66100
2.19-2.2556.090.48873.651161611616190819080.895-0.0630.21150.53440.72994.399.794.399.794.33.299.7
2.133-2.197.280.60563.431387613876190719070.876-0.050.2410.65230.7511001001001001003.69100
2.08-2.1337.290.704931391213912190819080.855-0.030.28020.75920.71898.998.998.998.998.93.6998.9
2.028-2.087.240.77312.781380713807190719070.844-0.0190.3080.83290.73392.992.792.991.992.23.6692.7
1.978-2.0287.260.85992.511384613846190819080.806-0.0730.34280.92660.71591.891.991.88585.33.6791.9
1.927-1.9787.250.94682.321381813818190719070.7820.0140.3781.02050.74590.890.990.876.476.83.6590.9
1.876-1.9277.181.11551.981369813698190819080.691-0.0190.44841.20370.74190.190.490.168.768.93.6390.4
1.819-1.8767.161.27031.711364613646190719070.64-0.0210.51141.37080.71282.882.682.854.454.83.682.6
1.699-1.8196.841.50151.431304713047190819080.555-0.0010.61781.62530.70151.951.951.921.221.33.4451.9

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Processing

Software
NameVersionClassification
autoPROC1.1.7data processing
XDSJan 31, 2020data reduction
Aimless0.7.15data scaling
STARANISO2.3.94data scaling
BUSTER2.11.8refinement
pointless1.12.16data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.699→32.99 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.104 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.11 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.102
RfactorNum. reflection% reflectionSelection details
Rfree0.2118 1885 -RANDOM
Rwork0.1854 ---
obs0.1867 38143 78.1 %-
Displacement parametersBiso mean: 20.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.3468 Å20 Å2-0.2999 Å2
2--0.5641 Å20 Å2
3----0.2173 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.699→32.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 95 300 2577
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092363HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.043229HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d788SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes420HARMONIC5
X-RAY DIFFRACTIONt_it2363HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion288SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2300SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.71
X-RAY DIFFRACTIONt_other_torsion18.18
LS refinement shellResolution: 1.7→1.78 Å
RfactorNum. reflection% reflection
Rfree0.2157 32 -
Rwork0.2418 --
obs0.2407 763 12.72 %

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