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- PDB-5yp7: p62/SQSTM1 ZZ domain -

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Basic information

Entry
Database: PDB / ID: 5yp7
Titlep62/SQSTM1 ZZ domain
ComponentsSequestosome-1
KeywordsSIGNALING PROTEIN / Complex / p62/SQSTM1 / ZZ domain / Autophagy / N-end rule
Function / homology
Function and homology information


brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / response to mitochondrial depolarisation / aggrephagy / Lewy body / negative regulation of toll-like receptor 4 signaling pathway / amphisome / regulation of protein complex stability ...brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / response to mitochondrial depolarisation / aggrephagy / Lewy body / negative regulation of toll-like receptor 4 signaling pathway / amphisome / regulation of protein complex stability / endosome organization / autophagy of mitochondrion / pexophagy / membraneless organelle assembly / phagophore assembly site / ubiquitin-modified protein reader activity / regulation of mitochondrion organization / regulation of canonical NF-kappaB signal transduction / Nuclear events mediated by NFE2L2 / aggresome / endosomal transport / intracellular membraneless organelle / K63-linked polyubiquitin modification-dependent protein binding / negative regulation of ferroptosis / temperature homeostasis / cellular response to stress / autolysosome / energy homeostasis / molecular sequestering activity / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Pexophagy / mitophagy / sperm midpiece / immune system process / inclusion body / signaling adaptor activity / negative regulation of protein ubiquitination / positive regulation of autophagy / PINK1-PRKN Mediated Mitophagy / ionotropic glutamate receptor binding / SH2 domain binding / autophagosome / protein sequestering activity / protein kinase C binding / sarcomere / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / positive regulation of protein localization to plasma membrane / macroautophagy / P-body / protein catabolic process / molecular condensate scaffold activity / PML body / receptor tyrosine kinase binding / Interleukin-1 signaling / autophagy / KEAP1-NFE2L2 pathway / Signaling by ALK fusions and activated point mutants / protein import into nucleus / late endosome / intracellular protein localization / Neddylation / signaling receptor activity / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / transcription by RNA polymerase II / cell differentiation / intracellular signal transduction / positive regulation of apoptotic process / intracellular membrane-bounded organelle / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / protein-containing complex binding / glutamatergic synapse / enzyme binding / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / 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 / : / PB1 domain profile. / Ubiquitin associated domain ...Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / : / UBA domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.424 Å
AuthorsKwon, D.H. / Kim, L. / Song, H.K.
CitationJournal: Nat Commun / Year: 2018
Title: Insights into degradation mechanism of N-end rule substrates by p62/SQSTM1 autophagy adapter.
Authors: Kwon, D.H. / Park, O.H. / Kim, L. / Jung, Y.O. / Park, Y. / Jeong, H. / Hyun, J. / Kim, Y.K. / Song, H.K.
History
DepositionNov 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sequestosome-1
D: Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9696
Polymers11,7072
Non-polymers2624
Water1,53185
1
A: Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9853
Polymers5,8541
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9853
Polymers5,8541
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.749, 43.345, 54.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11D-330-

HOH

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Components

#1: Protein Sequestosome-1 / EBI3-associated protein of 60 kDa / p60 / Phosphotyrosine-independent ligand for the Lck SH2 domain ...EBI3-associated protein of 60 kDa / p60 / Phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa / Ubiquitin-binding protein p62


Mass: 5853.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SQSTM1, ORCA, OSIL / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q13501
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 1.74 Å3/Da / Density % sol: 29.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Bis Tris, PEG MME 200, PEG 600

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.42→33.82 Å / Num. obs: 15680 / % possible obs: 99 % / Redundancy: 5.9 % / Net I/σ(I): 41.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.424→33.82 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5
RfactorNum. reflection% reflection
Rfree0.2072 1568 10 %
Rwork0.1866 --
obs0.1887 15676 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.424→33.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms648 0 4 85 737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013678
X-RAY DIFFRACTIONf_angle_d1.322894
X-RAY DIFFRACTIONf_dihedral_angle_d12.594240
X-RAY DIFFRACTIONf_chiral_restr0.09498
X-RAY DIFFRACTIONf_plane_restr0.007116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4235-1.46950.2921360.32781226X-RAY DIFFRACTION97
1.4695-1.5220.26031420.2721271X-RAY DIFFRACTION100
1.522-1.58290.30571420.24991290X-RAY DIFFRACTION100
1.5829-1.6550.25081410.22151271X-RAY DIFFRACTION100
1.655-1.74220.24721430.19061285X-RAY DIFFRACTION100
1.7422-1.85140.18541420.18431273X-RAY DIFFRACTION100
1.8514-1.99430.2141430.18771290X-RAY DIFFRACTION100
1.9943-2.1950.23361440.18631284X-RAY DIFFRACTION100
2.195-2.51250.21741460.17581315X-RAY DIFFRACTION100
2.5125-3.16510.20761470.17781328X-RAY DIFFRACTION100
3.1651-34.75930.17211420.1741275X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.28830.2062-0.38530.6058-0.60160.7450.2610.00560.0688-0.0664-0.2381-0.3195-0.09940.06550.00390.18510.00590.0030.20430.01970.2711152.9831166.8077232.3668
21.0472-0.36020.14221.5031-1.26331.08410.27670.1666-0.02760.0092-0.12410.01490.1770.1763-00.22130.014-0.02050.1902-0.02370.197147.573161.591235.7609
30.68190.4616-0.06420.4413-0.47131.43010.2044-0.3264-0.07350.1995-0.0269-0.02270.1013-0.08420.0140.16240.0017-0.01560.2241-0.02810.2189144.7149161.7506239.6866
40.55490.53150.14150.50670.110.30040.19870.0889-0.08860.05340.2064-0.04330.37650.70870.00020.23570.0483-0.03110.3268-0.01870.2345143.116181.6251230.1836
50.55520.07380.15810.36370.1540.59960.34330.41360.00120.01-0.0456-0.1074-0.295-0.18140.00120.25510.05020.05340.23670.02840.2425148.1539189.2961233.4591
60.6330.1859-0.45210.34660.0790.47310.38020.27-0.06730.1909-0.236-0.27860.00550.12880.00160.20880.0178-0.03580.19990.00280.2846153.2861182.2655236.5732
74.9772.7011-0.82251.9830.23111.4847-0.56720.35210.5833-0.15650.22350.093-0.5219-0.2687-0.86090.20310.02490.02150.24530.02960.1727144.3008189.0343240.3941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 126 through 138 )
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 156 )
3X-RAY DIFFRACTION3chain 'A' and (resid 157 through 169 )
4X-RAY DIFFRACTION4chain 'D' and (resid 126 through 138 )
5X-RAY DIFFRACTION5chain 'D' and (resid 139 through 151 )
6X-RAY DIFFRACTION6chain 'D' and (resid 152 through 164 )
7X-RAY DIFFRACTION7chain 'D' and (resid 165 through 169 )

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