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- PDB-4cxt: BTB domain of KEAP1 in complex with CDDO -

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Basic information

Entry
Database: PDB / ID: 4cxt
TitleBTB domain of KEAP1 in complex with CDDO
ComponentsKELCH-LIKE ECH-ASSOCIATED PROTEIN 1
KeywordsSIGNALING PROTEIN / BTB DOMAIN / KEAP1
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
Chem-SXJ / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.66 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 8, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,7872
Polymers15,2941
Non-polymers4941
Water43224
1
A: KELCH-LIKE ECH-ASSOCIATED PROTEIN 1
hetero molecules

A: KELCH-LIKE ECH-ASSOCIATED PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5754
Polymers30,5872
Non-polymers9872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area5840 Å2
ΔGint-37.9 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.687, 42.687, 271.028
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2011-

HOH

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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: 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.: 1 / Source method: obtained synthetically / Formula: C31H43NO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45 % / 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: Nov 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.66→45.17 Å / Num. obs: 4283 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 17.4 % / Biso Wilson estimate: 82.41 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.5

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.66→45.17 Å / Cor.coef. Fo:Fc: 0.9386 / Cor.coef. Fo:Fc free: 0.9408 / SU R Cruickshank DPI: 1.057 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.322 / SU Rfree Cruickshank DPI: 0.302
RfactorNum. reflection% reflectionSelection details
Rfree0.24 262 5.43 %RANDOM
Rwork0.2106 ---
obs0.2122 4823 100 %-
Displacement parametersBiso mean: 82.604 Å2
Baniso -1Baniso -2Baniso -3
1--7.4051 Å20 Å20 Å2
2---7.4051 Å20 Å2
3---14.8103 Å2
Refine analyzeLuzzati coordinate error obs: 0.478 Å
Refinement stepCycle: LAST / Resolution: 2.66→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1029 0 36 24 1089
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091128HARMONIC2
X-RAY DIFFRACTIONt_angle_deg11573HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d396SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes33HARMONIC2
X-RAY DIFFRACTIONt_gen_planes156HARMONIC5
X-RAY DIFFRACTIONt_it1128HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion5.33
X-RAY DIFFRACTIONt_other_torsion18.08
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion145SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1308SEMIHARMONIC4
LS refinement shellResolution: 2.66→2.97 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3502 77 5.97 %
Rwork0.2321 1212 -
all0.2389 1289 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 7.8996 Å / Origin y: -10.0312 Å / Origin z: -15.5259 Å
111213212223313233
T0.0679 Å20.0685 Å20.0276 Å2--0.2359 Å2-0.0162 Å2---0.189 Å2
L1.9056 °2-1.9065 °2-0.3957 °2-3.3564 °22.345 °2--4.4833 °2
S-0.1714 Å °0.0132 Å °0.0124 Å °0.3307 Å °0.0439 Å °0.2015 Å °-0.4169 Å °-0.0052 Å °0.1274 Å °
Refinement TLS groupSelection details: CHAIN A AND RESIDUES 49-179

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