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- PDB-7k2f: Kelch domain of human KEAP1 bound to Nrf2 cyclic peptide, c[GAEETGE] -

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Basic information

Entry
Database: PDB / ID: 7k2f
TitleKelch domain of human KEAP1 bound to Nrf2 cyclic peptide, c[GAEETGE]
Components
  • Kelch-like ECH-associated protein 1
  • Nrf2 cyclic peptide,c[GAEETGE]
KeywordsPROTEIN BINDING / Peptide inhibitor / Inhibitor complex / Loop-mimic / cyclic peptide
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 / ubiquitin-like ligase-substrate adaptor activity / transcription regulator inhibitor activity / inclusion body / cellular response to interleukin-4 / actin filament / centriolar satellite ...regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / 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 / 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 / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / Ub-specific processing proteases / regulation of autophagy / protein ubiquitination / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Kelch-like ECH-associated protein 1 / : / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch motif / Kelch / Kelch repeat type 1 ...Kelch-like ECH-associated protein 1 / : / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch motif / Kelch / 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
Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsMuellers, S.N. / Allen, K.N.
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Recapitulating the Binding Affinity of Nrf2 for KEAP1 in a Cyclic Heptapeptide, Guided by NMR, X-ray Crystallography, and Machine Learning.
Authors: Ortet, P.C. / Muellers, S.N. / Viarengo-Baker, L.A. / Streu, K. / Szymczyna, B.R. / Beeler, A.B. / Allen, K.N. / Whitty, A.
History
DepositionSep 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

Downloads & links

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Assembly

Deposited unit
X: Kelch-like ECH-associated protein 1
A: Kelch-like ECH-associated protein 1
C: Nrf2 cyclic peptide,c[GAEETGE]


Theoretical massNumber of molelcules
Total (without water)74,7223
Polymers74,7223
Non-polymers00
Water00
1
X: Kelch-like ECH-associated protein 1


Theoretical massNumber of molelcules
Total (without water)37,0151
Polymers37,0151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11790 Å2
MethodPISA
2
A: Kelch-like ECH-associated protein 1
C: Nrf2 cyclic peptide,c[GAEETGE]


Theoretical massNumber of molelcules
Total (without water)37,7072
Polymers37,7072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint0 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.635, 68.888, 144.018
Angle α, β, γ (deg.)90.000, 90.950, 90.000
Int Tables number5
Space group name H-MI121

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Components

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


Mass: 37015.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145
#2: Protein/peptide Nrf2 cyclic peptide,c[GAEETGE]


Mass: 691.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 1.2 - 1.5 M Ammonium Sulfate, 0.5-0.7% PEG-MME-550, 0.1 M Bis-Tris pH = 6.0 - 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9767 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9767 Å / Relative weight: 1
ReflectionResolution: 2.37→27.15 Å / Num. obs: 30738 / % possible obs: 98.79 % / Redundancy: 1.8 % / Biso Wilson estimate: 38.77 Å2 / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.04921 / Rpim(I) all: 0.04921 / Rrim(I) all: 0.06959 / Net I/σ(I): 10.48
Reflection shellResolution: 2.37→2.455 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.2256 / Mean I/σ(I) obs: 3.11 / Num. unique obs: 5486 / CC1/2: 0.87 / CC star: 0.965 / Rpim(I) all: 0.2256 / Rrim(I) all: 0.3191 / % possible all: 98.48

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WFL

5wfl


Resolution: 2.37→27.15 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 1017 3.31 %
Rwork0.237 29677 -
obs0.2378 30694 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.11 Å2 / Biso mean: 38.7699 Å2 / Biso min: 5.72 Å2
Refinement stepCycle: final / Resolution: 2.37→27.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4391 0 0 0 4391
Num. residues----577
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.37-2.490.36821450.30544205435099
2.49-2.650.35951420.30194249439199
2.65-2.860.33511430.28314140428398
2.86-3.140.2571440.25524278442299
3.14-3.60.23551500.24134217436799
3.6-4.530.19331450.19394248439398
4.53-27.150.26861480.20244340448899

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