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- PDB-6miu: Crystal structure of p62 ZZ domain in complex with Arg-Glu peptide -

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Basic information

Entry
Database: PDB / ID: 6miu
TitleCrystal structure of p62 ZZ domain in complex with Arg-Glu peptide
ComponentsSequestosome-1, Arg-Glu peptide chimera
KeywordsSIGNALING PROTEIN / p62 / ZZ domain / Nt-degron / autophagy / receptor
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 / Lewy body / response to mitochondrial depolarisation / aggrephagy / amphisome / negative regulation of toll-like receptor 4 signaling pathway / pexophagy ...brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / Lewy body / response to mitochondrial depolarisation / aggrephagy / amphisome / negative regulation of toll-like receptor 4 signaling pathway / pexophagy / regulation of protein complex stability / autophagy of mitochondrion / endosome organization / non-membrane-bounded organelle assembly / molecular sequestering activity / phagophore assembly site / regulation of mitochondrion organization / aggresome / regulation of canonical NF-kappaB signal transduction / ubiquitin-modified protein reader activity / Nuclear events mediated by NFE2L2 / autolysosome / K63-linked polyubiquitin modification-dependent protein binding / intracellular non-membrane-bounded organelle / endosomal transport / temperature homeostasis / immune system process / mitophagy / autophagosome / positive regulation of autophagy / energy homeostasis / signaling adaptor activity / inclusion body / sperm midpiece / negative regulation of protein ubiquitination / protein sequestering activity / p75NTR recruits signalling complexes / PINK1-PRKN Mediated Mitophagy / Pexophagy / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / sarcomere / SH2 domain binding / molecular condensate scaffold activity / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / macroautophagy / protein kinase C binding / positive regulation of protein localization to plasma membrane / ionotropic glutamate receptor binding / P-body / protein catabolic process / protein localization / receptor tyrosine kinase binding / PML body / autophagy / Interleukin-1 signaling / protein import into nucleus / KEAP1-NFE2L2 pathway / Signaling by ALK fusions and activated point mutants / late endosome / protein-macromolecule adaptor activity / Neddylation / signaling receptor activity / 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 / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding / cytoplasm / cytosol
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. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / UBA-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsAhn, J. / Zhang, Y. / Kutateladze, T.G.
CitationJournal: Nat Commun / Year: 2018
Title: ZZ-dependent regulation of p62/SQSTM1 in autophagy.
Authors: Zhang, Y. / Mun, S.R. / Linares, J.F. / Ahn, J. / Towers, C.G. / Ji, C.H. / Fitzwalter, B.E. / Holden, M.R. / Mi, W. / Shi, X. / Moscat, J. / Thorburn, A. / Diaz-Meco, M.T. / Kwon, Y.T. / Kutateladze, T.G.
History
DepositionSep 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 13, 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

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Assembly

Deposited unit
A: Sequestosome-1, Arg-Glu peptide chimera
B: Sequestosome-1, Arg-Glu peptide chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5186
Polymers12,2562
Non-polymers2624
Water2,396133
1
A: Sequestosome-1, Arg-Glu peptide chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2593
Polymers6,1281
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sequestosome-1, Arg-Glu peptide chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2593
Polymers6,1281
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.990, 27.864, 38.994
Angle α, β, γ (deg.)90.06, 90.45, 110.30
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Sequestosome-1, Arg-Glu peptide chimera / 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: 6128.055 Da / Num. of mol.: 2 / Fragment: ZZ-type residues 120-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SQSTM1, ORCA, OSIL / Production host: Escherichia coli (E. coli) / References: UniProt: Q13501
#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M BICINE, pH 8.0, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→25.313 Å / Num. obs: 51427 / % possible obs: 99.5 % / Redundancy: 6.1 % / CC1/2: 0.955 / Rmerge(I) obs: 0.064 / Net I/σ(I): 27.8
Reflection shellResolution: 1.9→1.93 Å / CC1/2: 0.955 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 1.9→25.313 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.99
Details: While refining the structure, the software used 14195 reflections automatically.
RfactorNum. reflection% reflection
Rfree0.2123 1477 10.41 %
Rwork0.1546 --
obs0.1606 14195 83.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→25.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms846 0 4 133 983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007912
X-RAY DIFFRACTIONf_angle_d1.081238
X-RAY DIFFRACTIONf_dihedral_angle_d11.149346
X-RAY DIFFRACTIONf_chiral_restr0.041131
X-RAY DIFFRACTIONf_plane_restr0.005167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8952-1.95640.2429830.1955690X-RAY DIFFRACTION49
1.9564-2.02630.24581050.1945857X-RAY DIFFRACTION65
2.0263-2.10740.24641240.17471039X-RAY DIFFRACTION74
2.1074-2.20320.22171200.16161125X-RAY DIFFRACTION82
2.2032-2.31930.24071430.1551212X-RAY DIFFRACTION88
2.3193-2.46450.24451420.16961288X-RAY DIFFRACTION92
2.4645-2.65460.2311450.1741319X-RAY DIFFRACTION93
2.6546-2.92140.22631360.17481265X-RAY DIFFRACTION94
2.9214-3.34330.2121640.15611313X-RAY DIFFRACTION95
3.3433-4.20910.19791530.13121288X-RAY DIFFRACTION95
4.2091-25.31520.17041620.13221322X-RAY DIFFRACTION95

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