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- PDB-7x4x: BTB domain of KEAP1 in complex with MEF -

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Basic information

Entry
Database: PDB / ID: 7x4x
TitleBTB domain of KEAP1 in complex with MEF
ComponentsKelch-like ECH-associated protein 1
KeywordsSIGNALING PROTEIN / KEAP1 / MEF
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 / Kelch repeat type 1 / Kelch motif / 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 / 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
Similarity search - Domain/homology
4-ethoxy-4-oxobutanoic acid / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsQu, L.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Characterization of the modification of Kelch-like ECH-associated protein 1 by different fumarates.
Authors: Qu, L. / Guo, M. / Zhang, H. / Chen, X. / Wei, H. / Jiang, L. / Li, J. / Chen, Z. / Dai, S. / Chen, Y.
History
DepositionMar 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Kelch-like ECH-associated protein 1
D: Kelch-like ECH-associated protein 1
C: Kelch-like ECH-associated protein 1
B: Kelch-like ECH-associated protein 1
A: Kelch-like ECH-associated protein 1
F: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,93612
Polymers93,0596
Non-polymers8776
Water0
1
E: Kelch-like ECH-associated protein 1
B: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3124
Polymers31,0202
Non-polymers2922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-35 kcal/mol
Surface area12300 Å2
MethodPISA
2
D: Kelch-like ECH-associated protein 1
C: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3124
Polymers31,0202
Non-polymers2922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-35 kcal/mol
Surface area12800 Å2
MethodPISA
3
A: Kelch-like ECH-associated protein 1
hetero molecules

F: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3124
Polymers31,0202
Non-polymers2922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_444-x-1/2,-y-1,z-1/21
Buried area3800 Å2
ΔGint-36 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.322, 99.289, 143.591
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15509.844 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14145
#2: Chemical
ChemComp-9J3 / 4-ethoxy-4-oxobutanoic acid


Mass: 146.141 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H10O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.23 Å3/Da / Density % sol: 61.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2 M lithium acetate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.58 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.58 Å / Relative weight: 1
ReflectionResolution: 2.96→19.39 Å / Num. obs: 25315 / % possible obs: 98.1 % / Redundancy: 5.1 % / CC1/2: 1 / Net I/σ(I): 8
Reflection shellResolution: 3→3.1 Å / Num. unique obs: 2191 / CC1/2: 0.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CXI

4cxi


Resolution: 2.96→19.39 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2606 1990 7.86 %
Rwork0.2031 23314 -
obs0.2076 25304 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.85 Å2 / Biso mean: 62.5059 Å2 / Biso min: 16.67 Å2
Refinement stepCycle: final / Resolution: 2.96→19.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5849 0 60 0 5909
Biso mean--92.61 --
Num. residues----773
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.96-3.030.34821140.30611331144579
3.03-3.110.36131410.290416571798100
3.11-3.20.32621410.26216531794100
3.2-3.310.31271420.255616671809100
3.31-3.430.31781440.254616801824100
3.43-3.560.28621420.227716571799100
3.56-3.720.27321440.214316901834100
3.72-3.920.28351420.216216691811100
3.92-4.160.22941450.193416921837100
4.16-4.480.28511440.167616941838100
4.48-4.920.22691450.164216831828100
4.92-5.620.25091460.199117201866100
5.62-7.020.25891470.226117291876100
7.02-19.390.1951530.15821792194599

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