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- PDB-7k2e: Kelch domain of human KEAP1 bound to Nrf2-based cyclic peptide, c... -

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Basic information

Entry
Database: PDB / ID: 7k2e
TitleKelch domain of human KEAP1 bound to Nrf2-based cyclic peptide, c[GDEETGE]
Components
  • GLY-ASP-GLU-GLU-THR-GLY-GLU
  • Kelch-like ECH-associated protein 1
KeywordsPROTEIN BINDING/Inhibitor / Peptide inhibitor / Inhibitor complex / Loop-mimic / PROTEIN BINDING / cyclic peptide / PROTEIN BINDING-Inhibitor complex
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 / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 / inclusion body / regulation of autophagy / actin filament ...regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 / inclusion body / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / Ub-specific processing proteases / protein ubiquitination / 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: 2.03 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

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Assembly

Deposited unit
A: Kelch-like ECH-associated protein 1
B: Kelch-like ECH-associated protein 1
P: GLY-ASP-GLU-GLU-THR-GLY-GLU


Theoretical massNumber of molelcules
Total (without water)66,7483
Polymers66,7483
Non-polymers00
Water2,216123
1
A: Kelch-like ECH-associated protein 1
P: GLY-ASP-GLU-GLU-THR-GLY-GLU


Theoretical massNumber of molelcules
Total (without water)33,7422
Polymers33,7422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-0 kcal/mol
Surface area11550 Å2
MethodPISA
2
B: Kelch-like ECH-associated protein 1


Theoretical massNumber of molelcules
Total (without water)33,0061
Polymers33,0061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.149, 68.872, 77.371
Angle α, β, γ (deg.)90.000, 117.476, 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: 33005.934 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 GLY-ASP-GLU-GLU-THR-GLY-GLU


Mass: 735.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 3.02 Å3/Da / Density % sol: 59.3 %
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: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.03→29.31 Å / Num. obs: 48405 / % possible obs: 98.91 % / Redundancy: 2 % / Biso Wilson estimate: 36.38 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.04294 / Rpim(I) all: 0.04294 / Rrim(I) all: 0.06073 / Net I/σ(I): 11.22
Reflection shellResolution: 2.031→2.104 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.4453 / Mean I/σ(I) obs: 1.88 / Num. unique obs: 4659 / CC1/2: 0.726 / CC star: 0.917 / Rpim(I) all: 0.4453 / Rrim(I) all: 0.6297 / % possible all: 95.42

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Processing

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

5wfl


Resolution: 2.03→29.31 Å / SU ML: 0.2627 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.2572
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2502 1992 4.12 %
Rwork0.2146 46396 -
obs0.2161 48388 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.86 Å2
Refinement stepCycle: LAST / Resolution: 2.03→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4364 0 0 123 4487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00744471
X-RAY DIFFRACTIONf_angle_d0.91166094
X-RAY DIFFRACTIONf_chiral_restr0.0621655
X-RAY DIFFRACTIONf_plane_restr0.0069806
X-RAY DIFFRACTIONf_dihedral_angle_d15.9718651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.080.35931340.30013183X-RAY DIFFRACTION95.56
2.08-2.140.32431400.27613245X-RAY DIFFRACTION98.63
2.14-2.20.29791420.25923293X-RAY DIFFRACTION98.65
2.2-2.270.28321400.24443296X-RAY DIFFRACTION98.79
2.27-2.350.25111450.23343320X-RAY DIFFRACTION98.92
2.35-2.450.27681430.243289X-RAY DIFFRACTION99.1
2.45-2.560.26081410.24043301X-RAY DIFFRACTION99.31
2.56-2.690.28341390.23193329X-RAY DIFFRACTION99.48
2.69-2.860.271480.22133343X-RAY DIFFRACTION99.54
2.86-3.080.25371450.22963315X-RAY DIFFRACTION99.68
3.08-3.390.25411380.2213357X-RAY DIFFRACTION99.46
3.39-3.880.24251460.20293347X-RAY DIFFRACTION99.63
3.88-4.890.19641430.16583366X-RAY DIFFRACTION99.49
4.89-29.310.24481480.21283412X-RAY DIFFRACTION99.11

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