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- PDB-4cxi: BTB domain of KEAP1 -

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Basic information

Entry
Database: PDB / ID: 4cxi
TitleBTB domain of KEAP1
ComponentsKELCH-LIKE ECH-ASSOCIATED PROTEIN 1
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity ...regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity / KEAP1-NFE2L2 pathway / disordered domain specific binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to oxidative stress / Neddylation / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / protein ubiquitination / Ub-specific processing proteases / endoplasmic reticulum / 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 / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Kelch repeat type 1 ...Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Kelch repeat type 1 / Kelch motif / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsCleasby, A. / Yon, J. / Day, P.J. / Richardson, C. / Tickle, I.J. / Williams, P.A. / Callahan, J.F. / Carr, R. / Concha, N. / Kerns, J.K. ...Cleasby, A. / Yon, J. / Day, P.J. / Richardson, C. / Tickle, I.J. / Williams, P.A. / Callahan, J.F. / Carr, R. / Concha, N. / Kerns, J.K. / Qi, H. / Sweitzer, T. / Ward, P. / Davies, T.G.
CitationJournal: Plos One / Year: 2014
Title: Structure of the Btb Domain of Keap1 and its Interaction with the Triterpenoid Antagonist Cddo.
Authors: Cleasby, A. / Yon, J. / Day, P.J. / Richardson, C. / Tickle, I.J. / Williams, P.A. / Callahan, J.F. / Carr, R. / Concha, N. / Kerns, J.K. / Qi, H. / Sweitzer, T. / Ward, P. / Davies, T.G.
History
DepositionApr 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KELCH-LIKE ECH-ASSOCIATED PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)15,2941
Polymers15,2941
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.807, 42.807, 266.506
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein KELCH-LIKE ECH-ASSOCIATED PROTEIN 1 / CYTOSOLIC INHIBITOR OF NRF2 / INRF2 / KELCH-LIKE PROTEIN 19 / KEAP1


Mass: 15293.651 Da / Num. of mol.: 1 / Fragment: BTB, RESIDUES 48-180 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14145
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsBTB DOMAIN ONLY

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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: 2.3 Å3/Da / Density % sol: 46.63 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.35→44.42 Å / Num. obs: 6383 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22

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Processing

Software
NameVersionClassification
REFMAC5.8.0064refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EOZ

4eoz


Resolution: 2.35→44.42 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 18.876 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25534 359 5.3 %RANDOM
Rwork0.18491 ---
obs0.18872 6363 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.249 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20.31 Å20 Å2
2--0.62 Å20 Å2
3----2 Å2
Refinement stepCycle: LAST / Resolution: 2.35→44.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1005 0 0 38 1043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191022
X-RAY DIFFRACTIONr_bond_other_d0.0010.02986
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.951380
X-RAY DIFFRACTIONr_angle_other_deg0.85532264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3575129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16925.22744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.76715182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.043153
X-RAY DIFFRACTIONr_chiral_restr0.090.2161
X-RAY DIFFRACTIONr_gen_planes_refined00.021156
X-RAY DIFFRACTIONr_gen_planes_other00.02231
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.04610.654519
X-RAY DIFFRACTIONr_mcbond_other8.03310.663518
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it9.55712.653502
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.486 21 -
Rwork0.287 457 -
obs--98.56 %
Refinement TLS params.Method: refined / Origin x: 6.8193 Å / Origin y: -9.7039 Å / Origin z: -14.8248 Å
111213212223313233
T0.2666 Å20.0645 Å20.0132 Å2-0.0512 Å2-0.0099 Å2--0.0209 Å2
L4.1494 °2-2.1859 °20.3166 °2-4.7372 °21.6401 °2--5.4051 °2
S-0.1223 Å °-0.2021 Å °0.1949 Å °0.3281 Å °0.0229 Å °0.0968 Å °-0.4348 Å °-0.0995 Å °0.0994 Å °

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