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- PDB-7xot: Crystal structure of Keap1_6k -

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Basic information

Entry
Database: PDB / ID: 7xot
TitleCrystal structure of Keap1_6k
ComponentsKelch-like ECH-associated protein 1
KeywordsPROTEIN BINDING / oxidative stress sensor
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
Chem-HB6 / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsXu, K.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of Keap1_6k
Authors: Xu, K.
History
DepositionMay 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)32,7122
Polymers31,9371
Non-polymers7761
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11490 Å2
Unit cell
Length a, b, c (Å)126.771, 76.309, 48.248
Angle α, β, γ (deg.)90.000, 105.622, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 31936.646 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: Chemical ChemComp-HB6 / 2-[[4-[(2-azanyl-2-oxidanylidene-ethyl)-(4-methoxyphenyl)sulfonyl-amino]naphthalen-1-yl]-[4-(2-diethoxyphosphorylethanoylamino)phenyl]sulfonyl-amino]ethanamide


Mass: 775.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H38N5O11PS2 / 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: 3.62 Å3/Da / Density % sol: 66.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 4.0M Ammonium acetate, 0.1M Tris-HCl, pH 8.8.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 12109 / % possible obs: 98.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 39.89 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 12.4
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.521 / Num. unique obs: 1198

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
Cootmodel building
PHENIXphasing
PHENIXv1.17.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XMB

4xmb


Resolution: 2.7→24.94 Å / SU ML: 0.3435 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.9261
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2367 2362 10.1 %
Rwork0.1757 21031 -
obs0.1817 12105 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.84 Å2
Refinement stepCycle: LAST / Resolution: 2.7→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 0 0 2217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00892338
X-RAY DIFFRACTIONf_angle_d1.14953193
X-RAY DIFFRACTIONf_chiral_restr0.06324
X-RAY DIFFRACTIONf_plane_restr0.0067416
X-RAY DIFFRACTIONf_dihedral_angle_d24.1151347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.750.29211330.25081176X-RAY DIFFRACTION93.63
2.75-2.810.26681400.2111245X-RAY DIFFRACTION97.95
2.81-2.880.27911370.19931228X-RAY DIFFRACTION97.15
2.88-2.950.29711390.2121224X-RAY DIFFRACTION97.71
2.95-3.030.31051440.21461283X-RAY DIFFRACTION98.01
3.03-3.120.27441350.21721223X-RAY DIFFRACTION97.35
3.12-3.220.30521400.20781242X-RAY DIFFRACTION97.81
3.22-3.330.28251360.18811226X-RAY DIFFRACTION97.63
3.33-3.470.26161440.16951261X-RAY DIFFRACTION98.32
3.47-3.620.23221360.16821215X-RAY DIFFRACTION96.98
3.62-3.810.23521410.18131235X-RAY DIFFRACTION98.36
3.81-4.050.221400.15541259X-RAY DIFFRACTION98.94
4.05-4.360.18031400.13391259X-RAY DIFFRACTION98.38
4.36-4.80.18241420.13811238X-RAY DIFFRACTION98.78
4.8-5.480.1981400.15541236X-RAY DIFFRACTION98.78
5.49-6.880.2591460.19621272X-RAY DIFFRACTION98.47
6.89-24.940.21631290.18541209X-RAY DIFFRACTION95.3

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