+Open data
-Basic information
Entry | Database: PDB / ID: 2flu | ||||||
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Title | Crystal Structure of the Kelch-Neh2 Complex | ||||||
Components |
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Keywords | LIGASE / Kelch domain / protein-peptide complex / beta-propeller | ||||||
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 / NFE2L2 regulating TCA cycle genes / positive regulation of ERAD pathway / 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 / NFE2L2 regulating TCA cycle genes / positive regulation of ERAD pathway / 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 / NFE2L2 regulating anti-oxidant/detoxification enzymes / NFE2L2 regulating tumorigenic genes / proteasomal ubiquitin-independent protein catabolic process / Cul3-RING ubiquitin ligase complex / regulation of innate immune response / regulation of embryonic development / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / positive regulation of blood vessel endothelial cell migration / cellular response to interleukin-4 / positive regulation of blood coagulation / cellular response to glucose starvation / 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 / cell redox homeostasis / regulation of autophagy / response to ischemia / transcription coregulator binding / actin filament / 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 / cellular response to hydrogen peroxide / positive regulation of neuron projection development / RNA polymerase II transcription regulator complex / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / disordered domain specific binding / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to xenobiotic stimulus / cellular response to oxidative stress / Neddylation / cellular response to tumor necrosis factor / midbody / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / DNA-binding transcription activator activity, RNA polymerase II-specific / proteasome-mediated ubiquitin-dependent protein catabolic process / 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: 1.5 Å | ||||||
Authors | Li, X. / Lo, J. / Beamer, L. / Hannink, M. | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: Structure of the Keap1:Nrf2 interface provides mechanistic insight into Nrf2 signaling. Authors: Lo, S.C. / Li, X. / Henzl, M.T. / Beamer, L.J. / Hannink, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2flu.cif.gz | 81 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2flu.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 2flu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/2flu ftp://data.pdbj.org/pub/pdb/validation_reports/fl/2flu | HTTPS FTP |
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-Related structure data
Related structure data | 1u6dS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33694.527 Da / Num. of mol.: 1 / Fragment: Kelch domain of human Keap1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: GenBank: 16198527, UniProt: Q14145*PLUS |
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#2: Protein/peptide | Mass: 1858.008 Da / Num. of mol.: 1 / Fragment: 16-mer peptide from huma Neh2 / Source method: obtained synthetically / Details: synthesized peptide / References: UniProt: Q16236 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 8.5 Details: 100 mM TrisHCl 200 mM MgCl2 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.23983 Å |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23983 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→36.4 Å / Num. obs: 50551 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.1 / % possible all: 64.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U6D Resolution: 1.5→36 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.491 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.076 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.535 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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