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- PDB-3wn7: Crystal Structure of Keap1 in Complex with the N-terminal region ... -

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Basic information

Entry
Database: PDB / ID: 3wn7
TitleCrystal Structure of Keap1 in Complex with the N-terminal region of the Nrf2 transcription factor
Components
  • Kelch-like ECH-associated protein 1
  • Peptide from Nuclear factor erythroid 2-related factor 2
KeywordsTRANSCRIPTION / beta-propeller / Kelch motif / Degron
Function / homology
Function and homology information


positive regulation of glutathione biosynthetic process / aflatoxin catabolic process / negative regulation of hematopoietic stem cell differentiation / Nuclear events mediated by NFE2L2 / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / negative regulation of cellular response to hypoxia / PERK-mediated unfolded protein response / cellular response to carbohydrate stimulus / regulation of cellular response to oxidative stress / regulation of removal of superoxide radicals ...positive regulation of glutathione biosynthetic process / aflatoxin catabolic process / negative regulation of hematopoietic stem cell differentiation / Nuclear events mediated by NFE2L2 / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / negative regulation of cellular response to hypoxia / PERK-mediated unfolded protein response / cellular response to carbohydrate stimulus / regulation of cellular response to oxidative stress / regulation of removal of superoxide radicals / KEAP1-NFE2L2 pathway / negative regulation of vascular associated smooth muscle cell migration / regulation of epidermal cell differentiation / Neddylation / cellular response to laminar fluid shear stress / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / cellular response to fluid shear stress / cellular response to angiotensin / negative regulation of cardiac muscle cell apoptotic process / regulation of innate immune response / Cul3-RING ubiquitin ligase complex / proteasomal ubiquitin-independent protein catabolic process / regulation of embryonic development / transcription factor binding / 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 / response to endoplasmic reticulum stress / cell redox homeostasis / response to organic substance / regulation of autophagy / actin filament / response to ischemia / transcription coregulator binding / protein-DNA complex / adherens junction / positive regulation of glucose import / 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 / disordered domain specific binding / cellular response to xenobiotic stimulus / cellular response to oxidative stress / 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 / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / protein ubiquitination / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of gene expression / focal adhesion / centrosome / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / Golgi apparatus / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
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 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch ...: / 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 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch repeat type 1 / Kelch motif / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / 6 Propeller / Neuraminidase / SKP1/BTB/POZ domain superfamily / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Nuclear factor erythroid 2-related factor 2 / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsFukutomi, T. / Takagi, K. / Mizushima, T. / Ohuchi, N. / Yamamoto, M.
CitationJournal: Mol.Cell.Biol. / Year: 2014
Title: Kinetic, thermodynamic, and structural characterizations of the association between Nrf2-DLGex degron and Keap1
Authors: Fukutomi, T. / Takagi, K. / Mizushima, T. / Ohuchi, N. / Yamamoto, M.
History
DepositionDec 5, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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: Peptide from Nuclear factor erythroid 2-related factor 2
L: Kelch-like ECH-associated protein 1
M: Peptide from Nuclear factor erythroid 2-related factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3286
Polymers77,2104
Non-polymers1182
Water8,809489
1
A: Kelch-like ECH-associated protein 1
B: Peptide from Nuclear factor erythroid 2-related factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6643
Polymers38,6052
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-6 kcal/mol
Surface area12730 Å2
MethodPISA
2
L: Kelch-like ECH-associated protein 1
M: Peptide from Nuclear factor erythroid 2-related factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6643
Polymers38,6052
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-5 kcal/mol
Surface area12600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.138, 84.394, 69.818
Angle α, β, γ (deg.)90.00, 116.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34270.109 Da / Num. of mol.: 2 / Fragment: Keap1-DC, UNP residues 321-609
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Keap1, Inrf2, Kiaa0132 / Plasmid: pET101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 Gold(DE3) / References: UniProt: Q9Z2X8
#2: Protein/peptide Peptide from Nuclear factor erythroid 2-related factor 2 / / NF-E2-related factor 2 / NFE2-related factor 2 / Nuclear factor / erythroid derived 2 / like 2


Mass: 4334.840 Da / Num. of mol.: 2 / Fragment: UNP residues 17-51 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q60795
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 100mM Sodium HEPES, 0.2M potassium acetate, 20% (w/v) PEG 3350, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 93450 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 18.6
Reflection shellResolution: 1.57→1.61 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 7.8 / % possible all: 88.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X2J

1x2j


Resolution: 1.57→34.78 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.421 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22299 4688 5 %RANDOM
Rwork0.18749 ---
obs0.18923 88724 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.864 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2---0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.57→34.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4796 0 8 489 5293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0195176
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3431.9367090
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2615683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00322.713247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21415796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3311550
X-RAY DIFFRACTIONr_chiral_restr0.1930.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0214118
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.574→1.614 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 336 -
Rwork0.213 5752 -
obs--88.54 %

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