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- PDB-7k2j: Kelch domain of human KEAP1 bound to Nrf2 cyclic peptide, c[GDPEAGE] -

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Basic information

Entry
Database: PDB / ID: 7k2j
TitleKelch domain of human KEAP1 bound to Nrf2 cyclic peptide, c[GDPEAGE]
Components
  • Kelch-like ECH-associated protein 1
  • Nrf2 cyclic peptide,c[GDPEAGE]
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 / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
B: Kelch-like ECH-associated protein 1
P: Nrf2 cyclic peptide,c[GDPEAGE]


Theoretical massNumber of molelcules
Total (without water)64,1613
Polymers64,1613
Non-polymers00
Water84747
1
A: Kelch-like ECH-associated protein 1


Theoretical massNumber of molelcules
Total (without water)31,7441
Polymers31,7441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11900 Å2
MethodPISA
2
B: Kelch-like ECH-associated protein 1
P: Nrf2 cyclic peptide,c[GDPEAGE]


Theoretical massNumber of molelcules
Total (without water)32,4172
Polymers32,4172
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-1 kcal/mol
Surface area12060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.178, 68.874, 77.398
Angle α, β, γ (deg.)90.000, 117.540, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 327 through 345 or (resid 346...
21chain B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUTYRTYR(chain A and (resid 327 through 345 or (resid 346...AA327 - 3453 - 21
12ASNASNASNASN(chain A and (resid 327 through 345 or (resid 346...AA34622
21LEULEUTHRTHRchain BBB327 - 6093 - 285

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Components

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


Mass: 31743.506 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[GDPEAGE]


Mass: 673.627 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.99 Å3/Da / Density % sol: 58.82 %
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: Jul 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9767 Å / Relative weight: 1
ReflectionResolution: 2.52→27.8 Å / Num. obs: 25220 / % possible obs: 97.84 % / Redundancy: 1.5 % / Biso Wilson estimate: 61.51 Å2 / CC1/2: 0.265 / CC star: 0.647 / Net I/σ(I): 3.04
Reflection shellResolution: 2.521→2.611 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 1.92 / Num. unique obs: 2424 / CC1/2: 0.0601 / % possible all: 94.94

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Processing

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

5wfl


Resolution: 2.52→27.78 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2738 1999 7.93 %
Rwork0.2241 23205 -
obs0.228 25204 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.19 Å2 / Biso mean: 61.0666 Å2 / Biso min: 21.96 Å2
Refinement stepCycle: final / Resolution: 2.52→27.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4375 0 0 47 4422
Biso mean---49.07 -
Num. residues----578
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1734X-RAY DIFFRACTION6.887TORSIONAL
12B1734X-RAY DIFFRACTION6.887TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.52-2.580.37461370.33061599173694
2.58-2.650.34491420.31291611175397
2.65-2.730.34961470.29031635178298
2.73-2.820.2931340.27751596173096
2.82-2.920.32471370.26791673181099
2.92-3.040.33751450.27271669181499
3.04-3.180.29761410.26171667180899
3.18-3.340.25981450.231616811826100
3.34-3.550.31611450.22841659180498
3.55-3.820.25261410.20341649179098
3.83-4.210.23321420.18551667180999
4.21-4.820.20311430.15971684182799
4.82-6.060.24821440.19881688183298
6.06-27.780.28741560.2381727188399

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