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- PDB-7c60: Crystal structure of Keap1 in complex with monoethyl fumarate (MEF) -

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Basic information

Entry
Database: PDB / ID: 7c60
TitleCrystal structure of Keap1 in complex with monoethyl fumarate (MEF)
ComponentsKelch-like ECH-associated protein 1
KeywordsCYTOSOLIC PROTEIN / beta-propeller domain / oxidative stress / Keap1-Nrf2 system / DMF / inhibitor complex
Function / homology
Function and homology information


regulation of epidermal cell differentiation / Neddylation / Ub-specific processing proteases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / transcription regulator inhibitor activity / inclusion body ...regulation of epidermal cell differentiation / Neddylation / Ub-specific processing proteases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / 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 / midbody / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of autophagy / protein ubiquitination / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein-containing complex / 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 motif / Kelch repeat type 1 / 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 motif / 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 / (~{Z})-4-ethoxy-4-oxidanylidene-but-2-enoic acid / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPadmanabhan, B. / Unni, S. / Deshmukh, P. / Krishnappa, G.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)DST-FIST: SR/FST/LS-I/2017(C) India
Science and Engineering Research Board (SERB)DST-FIST: SR/FST/LS-I/2017(C) India
CitationJournal: Febs J. / Year: 2021
Title: Structural insights into the multiple binding modes of Dimethyl Fumarate (DMF) and its analogs to the Kelch domain of Keap1.
Authors: Unni, S. / Deshmukh, P. / Krishnappa, G. / Kommu, P. / Padmanabhan, B.
History
DepositionMay 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)34,6536
Polymers34,1131
Non-polymers5395
Water8,845491
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-27 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.726, 103.726, 56.795
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 34113.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Keap1, Inrf2, Kiaa0132 / Plasmid: pET 28a / Details (production host): Histag / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z2X8
#2: Chemical ChemComp-NF3 / (~{Z})-4-ethoxy-4-oxidanylidene-but-2-enoic acid


Mass: 144.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / Source method: isolated from a natural source / Formula: H2O
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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Lithium Sulphate, PEG 8000, Sodium acetate, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54056 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Oct 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 1.6→24.95 Å / Num. obs: 26285 / % possible obs: 94.2 % / Redundancy: 8 % / Biso Wilson estimate: 10.14 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.14 / Net I/σ(I): 8
Reflection shellResolution: 1.6→1.97 Å / Num. unique obs: 1377 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X2J

1x2j


Resolution: 1.95→20.88 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2883 1172 4.96 %
Rwork0.214 22453 -
obs0.2177 23625 92.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.94 Å2 / Biso mean: 26.8085 Å2 / Biso min: 10.48 Å2
Refinement stepCycle: final / Resolution: 1.95→20.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2261 0 34 501 2796
Biso mean--42.45 35.47 -
Num. residues----297
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.040.43021470.28322721286891
2.04-2.150.28841560.23382957311399
2.15-2.280.45081290.33272568269785
2.28-2.460.40131230.32242483260682
2.46-2.70.37521500.2552922307297
2.7-3.090.28091580.21892898305696
3.09-3.890.24661490.1642859300894
3.89-20.880.19181600.15673045320598

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