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- PDB-2k0b: NMR structure of the UBA domain of p62 (SQSTM1) -

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Basic information

Entry
Database: PDB / ID: 2k0b
TitleNMR structure of the UBA domain of p62 (SQSTM1)
ComponentsSequestosome-1
KeywordsSIGNALING PROTEIN / ubiquitin binding / helical bundle / three helices / Alternative splicing / Apoptosis / Cytoplasm / Differentiation / Disease mutation / Endosome / Immune response / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Zinc / Zinc-finger
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 / endosomal transport / aggresome / intracellular membraneless organelle / K63-linked polyubiquitin modification-dependent protein binding / negative regulation of ferroptosis / temperature homeostasis / cellular response to stress / autolysosome / molecular sequestering activity / immune system process / mitophagy / energy homeostasis / sperm midpiece / inclusion body / signaling adaptor activity / negative regulation of protein ubiquitination / ionotropic glutamate receptor binding / positive regulation of autophagy / p75NTR recruits signalling complexes / SH2 domain binding / NF-kB is activated and signals survival / autophagosome / protein sequestering activity / Pexophagy / NRIF signals cell death from the nucleus / protein kinase C binding / sarcomere / positive regulation of long-term synaptic potentiation / ubiquitin binding / PINK1-PRKN Mediated Mitophagy / 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 / autophagy / Interleukin-1 signaling / protein import into nucleus / KEAP1-NFE2L2 pathway / Signaling by ALK fusions and activated point mutants / late endosome / intracellular protein localization / signaling receptor activity / Neddylation / 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-containing complex binding / protein kinase 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 (UBA) domain ...Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / : / UBA domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Ubiquitin-associated (UBA) 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 / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLong, J.E. / Ciani, B. / Gallagher, T.R.A. / Cavey, J.R. / Sheppard, P.W. / Layfield, R. / Searle, M.S.
CitationJournal: Proteins / Year: 2007
Title: Conformation and dynamics of the three-helix bundle UBA domain of p62 from experiment and simulation.
Authors: Evans, C.L. / Long, J.E. / Gallagher, T.R. / Hirst, J.D. / Searle, M.S.
History
DepositionJan 31, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)5,7441
Polymers5,7441
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 5744.406 Da / Num. of mol.: 1 / Fragment: UBA domain (UNP residues 387-436)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SQSTM1, ORCA, OSIL / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / 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: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1322D 1H-13C HSQC
1423D CBCA(CO)NH
1523D HN(CA)CB
1623D HNCO
1723D HN(CA)CO
1823D (H)CCH-TOCSY
1923D 1H-13C NOESY
11013D 1H-15N TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] Sequestosome-1, 50 mM potassium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] Sequestosome-1, 50 mM potassium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSequestosome-1[U-100% 15N]1
50 mMpotassium phosphate1
50 mMsodium chloride1
1 mMSequestosome-1[U-100% 13C; U-100% 15N]2
50 mMpotassium phosphate2
50 mMsodium chloride2
Sample conditionspH: 7 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.14Schwieters, Kuszewski, Tjandra and Clorestructure solution
TALOSCornilescu, Delaglio and Baxdata analysis
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
CcpNMR1.0.10CCPNchemical shift assignment
CcpNMR1.0.10CCPNdata analysis
CcpNMR1.0.10CCPNpeak picking
X-PLOR NIH2.14Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1078 / NOE intraresidue total count: 360 / NOE long range total count: 213 / NOE medium range total count: 246 / NOE sequential total count: 259 / Protein phi angle constraints total count: 36 / Protein psi angle constraints total count: 36
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30

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