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- PDB-2jy8: NMR structure of the ubiquitin associated (UBA) domain of p62 (SQ... -

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Basic information

Entry
Database: PDB / ID: 2jy8
TitleNMR structure of the ubiquitin associated (UBA) domain of p62 (SQSTM1) in complex with ubiquitin. RDC refined
ComponentsUbiquitin-binding protein p62
KeywordsPROTEIN BINDING / ubiquitin binding / ubiquitin associated domain / 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 / 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 / molecular sequestering activity / non-membrane-bounded organelle assembly / phagophore assembly site / regulation of mitochondrion organization / aggresome / regulation of canonical NF-kappaB signal transduction / Nuclear events mediated by NFE2L2 / ubiquitin-modified protein reader activity / autolysosome / K63-linked polyubiquitin modification-dependent protein binding / endosomal transport / intracellular non-membrane-bounded organelle / temperature homeostasis / immune system process / mitophagy / autophagosome / positive regulation of autophagy / signaling adaptor activity / energy homeostasis / inclusion body / negative regulation of protein ubiquitination / sperm midpiece / 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 / Signaling by ALK fusions and activated point mutants / receptor tyrosine kinase binding / PML body / autophagy / Interleukin-1 signaling / protein import into nucleus / KEAP1-NFE2L2 pathway / 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 / 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. / Ubiquitin-associated domain ...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. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / 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. / UBA-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLong, J.E. / Layfield, R. / Searle, M.S.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Ubiquitin Recognition by the Ubiquitin-associated Domain of p62 Involves a Novel Conformational Switch
Authors: Long, J. / Gallagher, T.R. / Cavey, J.R. / Sheppard, P.W. / Ralston, S.H. / Layfield, R. / Searle, M.S.
History
DepositionDec 7, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 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: Ubiquitin-binding protein p62


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_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 5744.406 Da / Num. of mol.: 1 / Fragment: UBA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SQSTM1, ORCA, OSIL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): (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 TOCSY
1313D 1H-15N NOESY
1422D 1H-13C HSQC
1523D HN(CA)CB
1623D CBCA(CO)NH
1723D (H)CCH-TOCSY
1823D 1H-13C NOESY
1923D HNCO
11023D HN(CA)CO
11132D 1H-15N HSQC-IPAP

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] protein, 50 mM potassium phosphate, 50 mM sodium chloride, 0.04 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] protein, 50 mM potassium phosphate, 50 mM sodium chloride, 0.04 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 15N] protein, 50 mM potassium phosphate, 50 mM sodium chloride, 0.04 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity[U-100% 15N]1
50 mMpotassium phosphate1
50 mMsodium chloride1
0.04 %sodium azide1
1 mMentity[U-100% 13C; U-100% 15N]2
50 mMpotassium phosphate2
50 mMsodium chloride2
0.04 %sodium azide2
1 mMentity[U-100% 15N]3
50 mMpotassium phosphate3
50 mMsodium chloride3
0.04 %sodium azide3
Sample conditionspH: 7 / Pressure: ambient / 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
XwinNMR3.5Bruker Biospincollection
XwinNMR3.5Bruker Biospinprocessing
CcpNMR1.0.10CCPNpeak picking
CcpNMR1.0.10CCPNdata analysis
CcpNMR1.0.10CCPNchemical shift assignment
TALOSCornilescu, Delaglio and Baxgeometry optimization
X-PLOR NIH2.14Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: In the first stage, high temperature Cartesian dynamics was performed at 1000 K with a time step of 0.005 ps, for 20,000 steps, using the Verlet integrator. During the second cooling phase ...Details: In the first stage, high temperature Cartesian dynamics was performed at 1000 K with a time step of 0.005 ps, for 20,000 steps, using the Verlet integrator. During the second cooling phase of the protocol, the temperature was reduced from 1000 K to 100 K in steps of 50 K, with a time step of 5 fs, over 40,000 steps during which the relative weighting of non-bonded energy terms were increased from 10% of their default values to their force field default. These initial structures were then refined with another 10000 cooling step
NMR constraintsNOE constraints total: 886 / NOE intraresidue total count: 341 / NOE long range total count: 85 / NOE medium range total count: 184 / NOE sequential total count: 204 / Protein phi angle constraints total count: 31 / Protein psi angle constraints total count: 31
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: 21

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