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- PDB-3ade: Crystal Structure of Keap1 in Complex with Sequestosome-1/p62 -

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Basic information

Entry
Database: PDB / ID: 3ade
TitleCrystal Structure of Keap1 in Complex with Sequestosome-1/p62
Components
  • Kelch-like ECH-associated protein 1
  • Sequestosome-1
KeywordsTRANSCRIPTION / BETA-PROPELLER / KELCH MOTIF
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 / NF-kB is activated and signals survival / Lewy body / response to mitochondrial depolarisation ...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 / NF-kB is activated and signals survival / Lewy body / response to mitochondrial depolarisation / aggrephagy / negative regulation of toll-like receptor 4 signaling pathway / amphisome / Interleukin-1 signaling / regulation of protein complex stability / endosome organization / regulation of epidermal cell differentiation / Neddylation / pexophagy / Ub-specific processing proteases / KEAP1-NFE2L2 pathway / membraneless organelle assembly / Antigen processing: Ubiquitination & Proteasome degradation / phagophore assembly site / ubiquitin-modified protein reader activity / regulation of canonical NF-kappaB signal transduction / negative regulation of response to oxidative stress / negative regulation of ferroptosis / aggresome / intracellular membraneless organelle / K63-linked polyubiquitin modification-dependent protein binding / Cul3-RING ubiquitin ligase complex / temperature homeostasis / transcription regulator inhibitor activity / immune system process / autolysosome / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / mitophagy / energy homeostasis / inclusion body / positive regulation of autophagy / ionotropic glutamate receptor binding / signaling adaptor activity / sperm midpiece / negative regulation of protein ubiquitination / protein sequestering activity / SH2 domain binding / cellular response to interleukin-4 / sarcomere / autophagosome / protein kinase C binding / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / regulation of autophagy / actin filament / positive regulation of protein localization to plasma membrane / transcription coregulator activity / macroautophagy / P-body / protein catabolic process / molecular condensate scaffold activity / PML body / autophagy / protein import into nucleus / disordered domain specific binding / late endosome / signaling receptor activity / midbody / ubiquitin-dependent protein catabolic process / cellular response to oxidative stress / protein-macromolecule adaptor activity / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / cell differentiation / protein ubiquitination / apoptotic process / ubiquitin protein ligase binding / regulation of DNA-templated transcription / protein-containing complex binding / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / 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 / : / PB1 domain profile. ...Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / : / UBA domain / Kelch-type beta propeller / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch motif / Kelch repeat type 1 / 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. / 6 Propeller / Neuraminidase / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / 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: 2.8 Å
AuthorsKurokawa, H. / Yamamoto, M.
CitationJournal: Nat.Cell Biol. / Year: 2010
Title: The selective autophagy substrate p62 activates the stress responsive transcription factor Nrf2 through inactivation of Keap1
Authors: Komatsu, M. / Kurokawa, H. / Waguri, S. / Taguchi, K. / Kobayashi, A. / Ichimura, Y. / Sou, Y.S. / Ueno, I. / Sakamoto, A. / Tong, K.I. / Kim, M. / Nishito, Y. / Iemura, S. / Natsume, T. / ...Authors: Komatsu, M. / Kurokawa, H. / Waguri, S. / Taguchi, K. / Kobayashi, A. / Ichimura, Y. / Sou, Y.S. / Ueno, I. / Sakamoto, A. / Tong, K.I. / Kim, M. / Nishito, Y. / Iemura, S. / Natsume, T. / Ueno, T. / Kominami, E. / Motohashi, H. / Tanaka, K. / Yamamoto, M.
History
DepositionJan 19, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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Assembly

Deposited unit
A: Kelch-like ECH-associated protein 1
B: Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,40211
Polymers36,5382
Non-polymers8659
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-1 kcal/mol
Surface area12120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.962, 102.962, 55.746
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 35006.277 Da / Num. of mol.: 1 / Fragment: Keap1-DC, UNP residues 309-624
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Inrf2, Keap1, Kiaa0132 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODONPLUS (DE3)_RIL / References: UniProt: Q9Z2X8
#2: Protein/peptide Sequestosome-1


Mass: 1531.641 Da / Num. of mol.: 1
Fragment: Keap1 Interacting Region (KIR), UNP residues 346-359
Source method: obtained synthetically / Details: Sequestosome-1 peptide / References: UniProt: Q64337
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 1.0M lithium sulfate, 0.5M ammonium sulfate, 0.1M sodium citrate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 8442 / Num. obs: 8442 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 58.3 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 19.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 6 / Num. unique all: 819 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X2J

1x2j


Resolution: 2.8→37.82 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 76209.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.232 878 10.7 %RANDOM
Rwork0.178 ---
obs0.178 8195 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.8072 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1--5.4 Å20 Å20 Å2
2---5.4 Å20 Å2
3---10.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.8→37.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 45 37 2354
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.252
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it3.182.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 135 10.4 %
Rwork0.237 1161 -
obs--93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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