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- PDB-8wfg: The Crystal Structure of KEAP1 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8wfg
TitleThe Crystal Structure of KEAP1 from Biortus.
ComponentsKelch-like ECH-associated protein 1
KeywordsTRANSCRIPTION / Host-virus interaction Ubl conjugation pathway
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
Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.251 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Shen, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of KEAP1 from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Shen, Z.
History
DepositionSep 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: 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


Theoretical massNumber of molelcules
Total (without water)14,8801
Polymers14,8801
Non-polymers00
Water81145
1
A: Kelch-like ECH-associated protein 1

A: Kelch-like ECH-associated protein 1


Theoretical massNumber of molelcules
Total (without water)29,7602
Polymers29,7602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area3900 Å2
ΔGint-31 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.647, 42.647, 266.672
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-236-

HOH

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Components

#1: Protein Kelch-like ECH-associated protein 1


Mass: 14880.175 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.14-0.24M lithium acetate, 18-21% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.25→36.93 Å / Num. obs: 7520 / % possible obs: 99.2 % / Redundancy: 28.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 28.6
Reflection shellResolution: 2.25→2.32 Å / Rmerge(I) obs: 1.02 / Num. unique obs: 654

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.251→36.93 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.041 / SU ML: 0.174 / Cross valid method: FREE R-VALUE / ESU R: 0.308 / ESU R Free: 0.231
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2646 403 5.36 %
Rwork0.2291 7116 -
all0.231 --
obs-7519 98.545 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 47.637 Å2
Baniso -1Baniso -2Baniso -3
1-0.916 Å20.458 Å20 Å2
2--0.916 Å2-0 Å2
3----2.973 Å2
Refinement stepCycle: LAST / Resolution: 2.251→36.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 0 45 1025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.013996
X-RAY DIFFRACTIONr_bond_other_d0.0010.016962
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.631343
X-RAY DIFFRACTIONr_angle_other_deg1.1921.5732209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7035123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.67923.54248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20915180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.078154
X-RAY DIFFRACTIONr_chiral_restr0.0580.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021115
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02225
X-RAY DIFFRACTIONr_nbd_refined0.1910.2185
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1640.2836
X-RAY DIFFRACTIONr_nbtor_refined0.1570.2481
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.2458
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.243
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1370.26
X-RAY DIFFRACTIONr_nbd_other0.1680.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.22
X-RAY DIFFRACTIONr_mcbond_it2.9034.769498
X-RAY DIFFRACTIONr_mcbond_other2.9014.764497
X-RAY DIFFRACTIONr_mcangle_it4.4687.12619
X-RAY DIFFRACTIONr_mcangle_other4.4657.125620
X-RAY DIFFRACTIONr_scbond_it3.4265.354498
X-RAY DIFFRACTIONr_scbond_other3.4225.355499
X-RAY DIFFRACTIONr_scangle_it5.5867.814724
X-RAY DIFFRACTIONr_scangle_other5.5827.816725
X-RAY DIFFRACTIONr_lrange_it7.97955.4721069
X-RAY DIFFRACTIONr_lrange_other7.9855.4281064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.251-2.3090.249240.297499X-RAY DIFFRACTION97.757
2.309-2.3720.392290.263502X-RAY DIFFRACTION97.9705
2.372-2.4410.333330.258447X-RAY DIFFRACTION98.1595
2.441-2.5160.277280.244471X-RAY DIFFRACTION97.8431
2.516-2.5980.369180.211430X-RAY DIFFRACTION97.6035
2.598-2.6890.283260.247466X-RAY DIFFRACTION98.2036
2.689-2.790.358230.257402X-RAY DIFFRACTION98.1524
2.79-2.9030.272180.233429X-RAY DIFFRACTION98.8938
2.903-3.0320.426200.257401X-RAY DIFFRACTION98.8263
3.032-3.1790.247280.225372X-RAY DIFFRACTION98.7654
3.179-3.350.243210.238368X-RAY DIFFRACTION98.9822
3.35-3.5520.264270.22355X-RAY DIFFRACTION98.4536
3.552-3.7950.256200.224324X-RAY DIFFRACTION99.422
3.795-4.0970.261170.207311X-RAY DIFFRACTION99.696
4.097-4.4840.178110.19301X-RAY DIFFRACTION99.6805
4.484-5.0070.239130.198274X-RAY DIFFRACTION99.6528
5.007-5.770.198130.255248X-RAY DIFFRACTION98.8636
5.77-7.0370.418140.278220X-RAY DIFFRACTION99.5745
7.037-9.8290.165140.177171X-RAY DIFFRACTION98.9305
9.829-36.930.31460.257125X-RAY DIFFRACTION97.037

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