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- PDB-3wdz: Crystal Structure of Keap1 in Complex with phosphorylated p62 -

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Basic information

Entry
Database: PDB / ID: 3wdz
TitleCrystal Structure of Keap1 in Complex with phosphorylated p62
Components
  • Kelch-like ECH-associated protein 1
  • Peptide from Sequestosome-1
KeywordsTRANSCRIPTION / Kelch repeat / p62 / Nucleus
Function / homology
Function and homology information


Pexophagy / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / PINK1-PRKN Mediated Mitophagy / protein targeting to vacuole involved in autophagy / Lewy body / NF-kB is activated and signals survival / aggrephagy ...Pexophagy / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / PINK1-PRKN Mediated Mitophagy / protein targeting to vacuole involved in autophagy / Lewy body / NF-kB is activated and signals survival / aggrephagy / response to mitochondrial depolarisation / cellular response to carbohydrate stimulus / amphisome / negative regulation of toll-like receptor 4 signaling pathway / non-membrane-bounded organelle assembly / Interleukin-1 signaling / KEAP1-NFE2L2 pathway / pexophagy / endosome organization / regulation of protein complex stability / regulation of epidermal cell differentiation / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / phagophore assembly site / aggresome / regulation of canonical NF-kappaB signal transduction / ubiquitin-modified protein reader activity / K63-linked polyubiquitin modification-dependent protein binding / autolysosome / temperature homeostasis / Cul3-RING ubiquitin ligase complex / immune system process / intracellular non-membrane-bounded organelle / mitophagy / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / autophagosome / signaling adaptor activity / positive regulation of autophagy / energy homeostasis / inclusion body / negative regulation of protein ubiquitination / sperm midpiece / ionotropic glutamate receptor binding / cellular response to interleukin-4 / molecular condensate scaffold activity / SH2 domain binding / sarcomere / protein sequestering activity / protein kinase C binding / ubiquitin binding / regulation of autophagy / positive regulation of long-term synaptic potentiation / actin filament / response to ischemia / P-body / transcription coregulator activity / positive regulation of protein localization to plasma membrane / macroautophagy / adherens junction / protein catabolic process / PML body / cellular response to reactive oxygen species / autophagy / protein import into nucleus / disordered domain specific binding / protein-macromolecule adaptor activity / late endosome / signaling receptor activity / cellular response to oxidative stress / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / cell differentiation / protein ubiquitination / positive regulation of protein phosphorylation / negative regulation of gene expression / focal adhesion / intracellular membrane-bounded organelle / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / UBA domain / Kelch-type beta propeller / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Kelch-like ECH-associated protein 1 / : ...Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / UBA domain / Kelch-type beta propeller / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / 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 / Ubiquitin associated domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Kelch-type beta propeller / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / 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
Sequestosome-1 / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFukutomi, T. / Takagi, K. / Mizushima, T. / Tanaka, K. / Komatsu, M. / Yamamoto, M.
CitationJournal: Mol.Cell / Year: 2013
Title: Phosphorylation of p62 activates the Keap1-Nrf2 pathway during selective autophagy.
Authors: Ichimura, Y. / Waguri, S. / Sou, Y.S. / Kageyama, S. / Hasegawa, J. / Ishimura, R. / Saito, T. / Yang, Y. / Kouno, T. / Fukutomi, T. / Hoshii, T. / Hirao, A. / Takagi, K. / Mizushima, T. / ...Authors: Ichimura, Y. / Waguri, S. / Sou, Y.S. / Kageyama, S. / Hasegawa, J. / Ishimura, R. / Saito, T. / Yang, Y. / Kouno, T. / Fukutomi, T. / Hoshii, T. / Hirao, A. / Takagi, K. / Mizushima, T. / Motohashi, H. / Lee, M.S. / Yoshimori, T. / Tanaka, K. / Yamamoto, M. / Komatsu, M.
History
DepositionJun 26, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references / Source and taxonomy
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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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: Peptide from Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)35,8822
Polymers35,8822
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-4 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.149, 75.149, 113.008
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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.: 1 / 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 Sequestosome-1 / / STONE14 / Ubiquitin-binding protein p62


Mass: 1611.620 Da / Num. of mol.: 1
Fragment: Keap1 Interacting Region (KIR), UNP residues 346-359
Source method: obtained synthetically / Details: Mouse / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q64337
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 100mM Tris-HCl (pH 8.8), 0.2M Sodium Nitrate, 20% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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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: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 11646 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.5
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 6.51 / % possible all: 98.8

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Processing

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

1x2j


Resolution: 2.6→42.67 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.917 / SU B: 11.195 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.546 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25491 551 4.7 %RANDOM
Rwork0.19081 ---
obs0.19367 11087 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.224 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å2-0.4 Å20 Å2
2---0.79 Å20 Å2
3---1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.6→42.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2276 0 0 5 2281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192330
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.943171
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2015294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89122.883111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00415345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1931521
X-RAY DIFFRACTIONr_chiral_restr0.1180.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211829
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.604→2.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 48 -
Rwork0.289 713 -
obs--99.09 %

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