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- PDB-5dad: Crystal Structure of Human KEAP1 BTB Domain in Complex with Small... -

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Basic information

Entry
Database: PDB / ID: 5dad
TitleCrystal Structure of Human KEAP1 BTB Domain in Complex with Small Molecule TX64014
ComponentsKelch-like ECH-associated protein 1
KeywordsTRANSCRIPTION / KEAP1 / Trascription Regulation / BTB domain / Cysteine Modification / C1-(R)-Cys151 adduct
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 / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 / inclusion body / regulation of autophagy / actin filament ...regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 / inclusion body / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity / 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 / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / Ub-specific processing proteases / protein ubiquitination / 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-TX6 / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsHuerta, C. / Jiang, X. / Trevino, I. / Bender, C.F. / Swinger, K.K. / Stoll, V.S. / Ferguson, D.A. / Thomas, P.J. / Probst, B. / Dulubova, I. ...Huerta, C. / Jiang, X. / Trevino, I. / Bender, C.F. / Swinger, K.K. / Stoll, V.S. / Ferguson, D.A. / Thomas, P.J. / Probst, B. / Dulubova, I. / Visnick, M. / Wigley, W.C.
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Characterization of novel small-molecule NRF2 activators: Structural and biochemical validation of stereospecific KEAP1 binding.
Authors: Huerta, C. / Jiang, X. / Trevino, I. / Bender, C.F. / Ferguson, D.A. / Probst, B. / Swinger, K.K. / Stoll, V.S. / Thomas, P.J. / Dulubova, I. / Visnick, M. / Wigley, W.C.
History
DepositionAug 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)15,8942
Polymers15,5951
Non-polymers2991
Water1629
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)31,7894
Polymers31,1902
Non-polymers5992
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+y,y,-z+1/31
Buried area3960 Å2
ΔGint-36 kcal/mol
Surface area12140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.220, 43.220, 135.171
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

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Components

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


Mass: 15594.950 Da / Num. of mol.: 1 / Fragment: BTB domain, residues 49-182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q14145
#2: Chemical ChemComp-TX6 / (6aS,7S,10aS)-8-hydroxy-4-methoxy-2,7,10a-trimethyl-5,6,6a,7,10,10a-hexahydrobenzo[h]quinazoline-9-carbonitrile


Mass: 299.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Potassium Thiocyanate, 30% w/v PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2012 / Details: Pixel
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.605→135.171 Å / Num. obs: 4678 / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 32 / Num. measured all: 44180
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all
2.605-2.61410.50.4625.541139
12.091-135.1716.80.0341561

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
XDSautoPROC, XDS (VERSION December 6, 2010)data scaling
PHASER2.3.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DAF

5daf


Resolution: 2.61→45.06 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.2442 / WRfactor Rwork: 0.1975 / FOM work R set: 0.7795 / SU B: 12.836 / SU ML: 0.256 / SU R Cruickshank DPI: 0.7813 / SU Rfree: 0.3063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.781 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2448 214 4.6 %RANDOM
Rwork0.2036 ---
obs0.2056 4431 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.91 Å2 / Biso mean: 63.438 Å2 / Biso min: 41.99 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20.68 Å20 Å2
2--1.35 Å20 Å2
3----2.03 Å2
Refinement stepCycle: final / Resolution: 2.61→45.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms959 0 22 9 990
Biso mean--79.77 54.97 -
Num. residues----123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.021000
X-RAY DIFFRACTIONr_angle_refined_deg0.9581.9821355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0755121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.67624.87841
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99915176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.327153
X-RAY DIFFRACTIONr_chiral_restr0.070.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02726
LS refinement shellResolution: 2.605→2.673 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 9 -
Rwork0.26 296 -
all-305 -
obs--100 %

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