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- PDB-6jm4: The crystal structure of PB1 homo-dimer of human P62/SQSTM1 -

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Basic information

Entry
Database: PDB / ID: 6jm4
TitleThe crystal structure of PB1 homo-dimer of human P62/SQSTM1
Components(Sequestosome-1) x 2
KeywordsSIGNALING PROTEIN / PB1 / P62/SQSTM1 / autophagy / PB1 dimer
Function / homology
Function and homology information


brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / protein targeting to vacuole involved in autophagy / regulation of Ras protein signal transduction / Lewy body / aggrephagy / response to mitochondrial depolarisation / amphisome / negative regulation of toll-like receptor 4 signaling pathway / non-membrane-bounded organelle assembly ...brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / protein targeting to vacuole involved in autophagy / regulation of Ras protein signal transduction / Lewy body / aggrephagy / response to mitochondrial depolarisation / amphisome / negative regulation of toll-like receptor 4 signaling pathway / non-membrane-bounded organelle assembly / pexophagy / endosome organization / regulation of protein complex stability / autophagy of mitochondrion / molecular sequestering activity / phagophore assembly site / regulation of mitochondrion organization / aggresome / regulation of canonical NF-kappaB signal transduction / ubiquitin-modified protein reader activity / K63-linked polyubiquitin modification-dependent protein binding / Nuclear events mediated by NFE2L2 / autolysosome / temperature homeostasis / endosomal transport / immune system process / intracellular non-membrane-bounded organelle / mitophagy / Signaling by ALK fusions and activated point mutants / autophagosome / signaling adaptor activity / positive regulation of autophagy / energy homeostasis / inclusion body / negative regulation of protein ubiquitination / sperm midpiece / ionotropic glutamate receptor binding / p75NTR recruits signalling complexes / PINK1-PRKN Mediated Mitophagy / Pexophagy / NRIF signals cell death from the nucleus / molecular condensate scaffold activity / NF-kB is activated and signals survival / SH2 domain binding / sarcomere / protein sequestering activity / protein kinase C binding / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / P-body / positive regulation of protein localization to plasma membrane / macroautophagy / protein catabolic process / protein localization / PML body / receptor tyrosine kinase binding / autophagy / Interleukin-1 signaling / protein import into nucleus / KEAP1-NFE2L2 pathway / protein-macromolecule adaptor activity / late endosome / signaling receptor activity / Neddylation / ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / cell differentiation / intracellular signal transduction / positive regulation of protein phosphorylation / positive regulation of apoptotic process / intracellular membrane-bounded organelle / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / UBA domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Ubiquitin associated domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. ...Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / UBA domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / 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. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.20014839602 Å
AuthorsShin, H.C. / Lim, D. / Kim, S.J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)2015M3A9B5030308 Korea, Republic Of
Ministry of Science, ICT and Future Planning Korea, Republic Of
CitationJournal: Mol.Cells / Year: 2019
Title: Oligomer Model of PB1 Domain of p62/SQSTM1 Based on Crystal Structure of Homo-Dimer and Calculation of Helical Characteristics.
Authors: Lim, D. / Lee, H.S. / Ku, B. / Shin, H.C. / Kim, S.J.
History
DepositionMar 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sequestosome-1
B: Sequestosome-1
D: Sequestosome-1
C: Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)45,2274
Polymers45,2274
Non-polymers00
Water0
1
A: Sequestosome-1
B: Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)22,6142
Polymers22,6142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Sequestosome-1
C: Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)22,6142
Polymers22,6142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.483, 53.517, 61.457
Angle α, β, γ (deg.)90.000, 94.287, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Sequestosome-1 / EBI3-associated protein of 60 kDa / p60 / Ubiquitin-binding protein p62


Mass: 11348.911 Da / Num. of mol.: 2 / Fragment: PB1 domain / Mutation: C26S, C27F, D69A, D71R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SQSTM1, ORCA, OSIL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13501
#2: Protein Sequestosome-1 / EBI3-associated protein of 60 kDa / p60 / Ubiquitin-binding protein p62


Mass: 11264.699 Da / Num. of mol.: 2 / Fragment: PB1 domain / Mutation: R21A, C26S, C27F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SQSTM1, ORCA, OSIL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13501

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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: 2.04 Å3/Da / Density % sol: 39.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.8 M DL-Malic acid (pH 7.0), 0.1 M Tris-HCl (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97943 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 3.2→48.3010675141 Å / Num. obs: 5366 / % possible obs: 87 % / Redundancy: 1.1 % / Biso Wilson estimate: 46.056916889 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0811 / Net I/σ(I): 10.54
Reflection shellResolution: 3.2→3.314 Å / Rmerge(I) obs: 0.2622 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2KKC

2kkc


Resolution: 3.20014839602→48.3010675141 Å / SU ML: 0.291546396471 / Cross valid method: FREE R-VALUE / σ(F): 1.65493830016 / Phase error: 25.8197531291
RfactorNum. reflection% reflection
Rfree0.276200471433 524 9.76518822214 %
Rwork0.238930609101 --
obs0.242593207011 5366 86.9974059663 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 50.5227148602 Å2
Refinement stepCycle: LAST / Resolution: 3.20014839602→48.3010675141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2410 0 0 0 2410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00248634959932455
X-RAY DIFFRACTIONf_angle_d0.4869862216193306
X-RAY DIFFRACTIONf_chiral_restr0.0384785800146373
X-RAY DIFFRACTIONf_plane_restr0.00357398303232418
X-RAY DIFFRACTIONf_dihedral_angle_d14.32951908321451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.52210.2817586338431120.2561167958371019X-RAY DIFFRACTION74.0667976424
3.5221-4.03150.289249581881240.2392803446721224X-RAY DIFFRACTION88.6259040105
4.0315-5.07840.2413452440661400.209662657321270X-RAY DIFFRACTION91.677503251
5.0784-48.30650.3024123912651480.260932880871329X-RAY DIFFRACTION93.4810126582
Refinement TLS params.Method: refined / Origin x: -28.5100700839 Å / Origin y: -23.5118514416 Å / Origin z: 13.9222891093 Å
111213212223313233
T0.0673961145355 Å2-0.0414367833578 Å2-0.0267300915994 Å2-0.0680621317795 Å20.00916546319911 Å2--0.0805745956292 Å2
L0.287664308499 °20.0889925737957 °2-0.133419168054 °2-0.356263640109 °2-0.0980664427673 °2--0.404826261484 °2
S-0.0179378705845 Å °-0.00774471844288 Å °0.0257271445108 Å °-0.0550404850464 Å °0.0756414470617 Å °0.0150250651931 Å °0.00857977134605 Å °0.0034666763593 Å °0.0322814378586 Å °
Refinement TLS groupSelection details: all

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