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- PDB-5wfv: Kelch domain of human Keap1 bound to Nrf2 ETGE peptide -

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Basic information

Entry
Database: PDB / ID: 5wfv
TitleKelch domain of human Keap1 bound to Nrf2 ETGE peptide
Components
  • Kelch-like ECH-associated protein 1
  • Nrf2 ETGE peptide
KeywordsTRANSCRIPTION / Scaffold / Peptide-bound
Function / homology
Function and homology information


positive regulation of glutathione biosynthetic process / aflatoxin catabolic process / negative regulation of hematopoietic stem cell differentiation / integrated stress response signaling / Regulation of HMOX1 expression and activity / negative regulation of cellular response to hypoxia / NFE2L2 regulating TCA cycle genes / positive regulation of ERAD pathway / PERK-mediated unfolded protein response / regulation of removal of superoxide radicals ...positive regulation of glutathione biosynthetic process / aflatoxin catabolic process / negative regulation of hematopoietic stem cell differentiation / integrated stress response signaling / Regulation of HMOX1 expression and activity / negative regulation of cellular response to hypoxia / NFE2L2 regulating TCA cycle genes / positive regulation of ERAD pathway / PERK-mediated unfolded protein response / regulation of removal of superoxide radicals / regulation of cellular response to oxidative stress / cellular response to laminar fluid shear stress / regulation of epidermal cell differentiation / NFE2L2 regulating ER-stress associated genes / NFE2L2 regulating inflammation associated genes / cellular response to methionine / mediator complex / cellular response to fluid shear stress / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / positive regulation of ubiquitin-dependent protein catabolic process / Regulation of NFE2L2 gene expression / Nuclear events mediated by NFE2L2 / negative regulation of cardiac muscle cell apoptotic process / negative regulation of response to oxidative stress / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / proteasomal ubiquitin-independent protein catabolic process / negative regulation of ferroptosis / Cul3-RING ubiquitin ligase complex / regulation of innate immune response / negative regulation of vascular associated smooth muscle cell migration / cellular response to angiotensin / regulation of embryonic development / positive regulation of blood vessel endothelial cell migration / positive regulation of blood coagulation / negative regulation of endothelial cell apoptotic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / transcription regulator inhibitor activity / endoplasmic reticulum unfolded protein response / cellular response to glucose starvation / ubiquitin-like ligase-substrate adaptor activity / inclusion body / reactive oxygen species metabolic process / cellular response to interleukin-4 / cell redox homeostasis / cellular response to copper ion / response to ischemia / transcription coregulator binding / positive regulation of D-glucose import across plasma membrane / actin filament / molecular condensate scaffold activity / Heme signaling / positive regulation of neuron projection development / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / protein-DNA complex / regulation of autophagy / RNA polymerase II transcription regulator complex / cellular response to xenobiotic stimulus / centriolar satellite / positive regulation of reactive oxygen species metabolic process / cellular response to hydrogen peroxide / positive regulation of angiogenesis / disordered domain specific binding / cellular response to tumor necrosis factor / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to oxidative stress / midbody / cellular response to hypoxia / sequence-specific DNA binding / ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / Ub-specific processing proteases / ciliary basal body / protein ubiquitination / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / inflammatory response / protein domain specific binding / ubiquitin protein ligase binding / positive regulation of gene expression / centrosome / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / Golgi apparatus / positive regulation of transcription by RNA polymerase II / DNA binding
Similarity search - Function
: / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Kelch-type beta propeller / Kelch-like ECH-associated protein 1 / : / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated ...: / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Kelch-type beta propeller / 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 / Kelch motif / Basic-leucine zipper (bZIP) domain signature. / Kelch repeat type 1 / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / 6 Propeller / Neuraminidase / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Mainly Beta
Similarity search - Domain/homology
Kelch-like ECH-associated protein 1 / Nuclear factor erythroid 2-related factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsCarolan, J.P. / Lynch, A.J. / Allen, K.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM118078 United States
CitationJournal: Biochemistry / Year: 2020
Title: Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2).
Authors: Zhong, M. / Lynch, A. / Muellers, S.N. / Jehle, S. / Luo, L. / Hall, D.R. / Iwase, R. / Carolan, J.P. / Egbert, M. / Wakefield, A. / Streu, K. / Harvey, C.M. / Ortet, P.C. / Kozakov, D. / ...Authors: Zhong, M. / Lynch, A. / Muellers, S.N. / Jehle, S. / Luo, L. / Hall, D.R. / Iwase, R. / Carolan, J.P. / Egbert, M. / Wakefield, A. / Streu, K. / Harvey, C.M. / Ortet, P.C. / Kozakov, D. / Vajda, S. / Allen, K.N. / Whitty, A.
History
DepositionJul 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 4, 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: Nrf2 ETGE peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9474
Polymers74,8503
Non-polymers961
Water2,072115
1
A: Kelch-like ECH-associated protein 1
P: Nrf2 ETGE peptide


Theoretical massNumber of molelcules
Total (without water)37,9512
Polymers37,9512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint1 kcal/mol
Surface area11920 Å2
MethodPISA
2
B: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9952
Polymers36,8991
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-12 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.919, 69.253, 79.228
Angle α, β, γ (deg.)90.00, 118.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 36899.176 Da / Num. of mol.: 2 / Fragment: UNP residues 320-612 / Mutation: E540A, E542A
Source method: isolated from a genetically manipulated source
Details: Histidine-tagged variant of human Keap1 Kelch domain, including mutations for altered crystallographic packing
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145
#2: Protein/peptide Nrf2 ETGE peptide


Mass: 1052.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16236*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 1.2 - 1.5 M Ammonium Sulfate, 0.1 M Bis-Tris pH = 6.0 - 6.5
PH range: 6.0 - 6.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen stream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 29, 2016
RadiationMonochromator: Cryo-Cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.69→52.14 Å / Num. obs: 58943 / % possible obs: 93 % / Redundancy: 3.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.06899 / Net I/σ(I): 15.18
Reflection shellResolution: 1.91→1.978 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.3304 / Mean I/σ(I) obs: 3.74 / Num. unique obs: 5843 / CC1/2: 0.886 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WLF

5wlf


Resolution: 1.91→52.14 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.13
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 1353 2.42 %Random selection
Rwork0.1995 ---
obs0.2002 55914 92.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.12 Å2
Refinement stepCycle: LAST / Resolution: 1.91→52.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4470 0 5 115 4590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074600
X-RAY DIFFRACTIONf_angle_d0.96267
X-RAY DIFFRACTIONf_dihedral_angle_d13.2272669
X-RAY DIFFRACTIONf_chiral_restr0.061670
X-RAY DIFFRACTIONf_plane_restr0.005827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.97830.28241330.25425239X-RAY DIFFRACTION89
1.9783-2.05750.28411300.23515310X-RAY DIFFRACTION91
2.0575-2.15120.26871370.2285398X-RAY DIFFRACTION92
2.1512-2.26460.22461350.22395350X-RAY DIFFRACTION92
2.2646-2.40650.26051420.21465554X-RAY DIFFRACTION95
2.4065-2.59230.28521410.23555583X-RAY DIFFRACTION95
2.5923-2.85320.31330.22635533X-RAY DIFFRACTION94
2.8532-3.2660.24921320.21835549X-RAY DIFFRACTION94
3.266-4.11480.18951310.18075422X-RAY DIFFRACTION92
4.1148-69.06020.17291390.15785623X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: -37.8434 Å / Origin y: -14.2627 Å / Origin z: 27.9836 Å
111213212223313233
T0.2061 Å2-0.0523 Å2-0.0083 Å2-0.2576 Å20.0383 Å2--0.2937 Å2
L-0.1689 °2-0.1315 °2-0.1649 °2--0.1071 °20.0104 °2--1.5889 °2
S0.0008 Å °-0.0527 Å °-0.0424 Å °0.0363 Å °-0.0251 Å °0.025 Å °0.0001 Å °-0.1049 Å °0.0288 Å °
Refinement TLS groupSelection details: all

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