+Open data
-Basic information
Entry | Database: PDB / ID: 5wfv | ||||||
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Title | Kelch domain of human Keap1 bound to Nrf2 ETGE peptide | ||||||
Components |
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Keywords | TRANSCRIPTION / 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 / Regulation of HMOX1 expression and activity / integrated stress response signaling / negative regulation of cellular response to hypoxia / positive regulation of ERAD pathway / NFE2L2 regulating TCA cycle genes / PERK-mediated unfolded protein response / regulation of cellular response to oxidative stress ...positive regulation of glutathione biosynthetic process / aflatoxin catabolic process / negative regulation of hematopoietic stem cell differentiation / Regulation of HMOX1 expression and activity / integrated stress response signaling / negative regulation of cellular response to hypoxia / positive regulation of ERAD pathway / NFE2L2 regulating TCA cycle genes / PERK-mediated unfolded protein response / regulation of cellular response to oxidative stress / regulation of removal of superoxide radicals / negative regulation of vascular associated smooth muscle cell migration / regulation of epidermal cell differentiation / cellular response to laminar fluid shear stress / NFE2L2 regulating ER-stress associated genes / positive regulation of ubiquitin-dependent protein catabolic process / NFE2L2 regulating inflammation associated genes / cellular response to fluid shear stress / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / cellular response to angiotensin / negative regulation of cardiac muscle cell apoptotic process / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / regulation of innate immune response / NFE2L2 regulating anti-oxidant/detoxification enzymes / NFE2L2 regulating tumorigenic genes / Cul3-RING ubiquitin ligase complex / proteasomal ubiquitin-independent protein catabolic process / regulation of embryonic development / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / positive regulation of blood vessel endothelial cell migration / cellular response to glucose starvation / positive regulation of blood coagulation / negative regulation of endothelial cell apoptotic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / inclusion body / endoplasmic reticulum unfolded protein response / cellular response to copper ion / cellular response to interleukin-4 / cell redox homeostasis / regulation of autophagy / actin filament / response to ischemia / transcription coregulator binding / protein-DNA complex / positive regulation of glucose import / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Heme signaling / negative regulation of DNA-binding transcription factor activity / positive regulation of neuron projection development / cellular response to hydrogen peroxide / RNA polymerase II transcription regulator complex / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / KEAP1-NFE2L2 pathway / disordered domain specific binding / cellular response to xenobiotic stimulus / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to oxidative stress / Neddylation / cellular response to tumor necrosis factor / midbody / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription activator activity, RNA polymerase II-specific / response to oxidative stress / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / sequence-specific DNA binding / protein ubiquitination / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / centrosome / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / Golgi apparatus / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Carolan, J.P. / Lynch, A.J. / Allen, K.N. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wfv.cif.gz | 238.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wfv.ent.gz | 190.8 KB | Display | PDB format |
PDBx/mmJSON format | 5wfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/5wfv ftp://data.pdbj.org/pub/pdb/validation_reports/wf/5wfv | HTTPS FTP |
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-Related structure data
Related structure data | 5wflC 5wg1C 5whlC 5whoC 5wiyC 5wlfS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | 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 | | 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 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.12 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Nitrogen stream |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 29, 2016 |
Radiation | Monochromator: Cryo-Cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WLF Resolution: 1.91→52.14 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.13
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→52.14 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -37.8434 Å / Origin y: -14.2627 Å / Origin z: 27.9836 Å
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Refinement TLS group | Selection details: all |