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- PDB-2rru: Solution structure of the UBA omain of p62 and its interaction wi... -

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Basic information

Entry
Database: PDB / ID: 2rru
TitleSolution structure of the UBA omain of p62 and its interaction with ubiquitin
ComponentsSequestosome-1
KeywordsPROTEIN BINDING / UBIQUITIN / UBA DOMAIN / P62/SQSTM1 / Autophagy
Function / homology
Function and homology information


Pexophagy / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / PINK1-PRKN Mediated Mitophagy / protein targeting to vacuole involved in autophagy / Lewy body / negative regulation of toll-like receptor 4 signaling pathway / non-membrane-bounded organelle assembly ...Pexophagy / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / PINK1-PRKN Mediated Mitophagy / protein targeting to vacuole involved in autophagy / Lewy body / negative regulation of toll-like receptor 4 signaling pathway / non-membrane-bounded organelle assembly / NF-kB is activated and signals survival / aggrephagy / response to mitochondrial depolarisation / amphisome / Interleukin-1 signaling / KEAP1-NFE2L2 pathway / pexophagy / endosome organization / regulation of protein complex stability / phagophore assembly site / aggresome / regulation of canonical NF-kappaB signal transduction / ubiquitin-modified protein reader activity / K63-linked polyubiquitin modification-dependent protein binding / autolysosome / temperature homeostasis / intracellular non-membrane-bounded organelle / immune system process / mitophagy / autophagosome / signaling adaptor activity / positive regulation of autophagy / energy homeostasis / inclusion body / negative regulation of protein ubiquitination / sperm midpiece / ionotropic glutamate receptor binding / molecular condensate scaffold activity / 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 / transcription coregulator activity / positive regulation of protein localization to plasma membrane / macroautophagy / protein catabolic process / PML body / autophagy / cellular response to reactive oxygen species / protein import into nucleus / protein-macromolecule adaptor activity / late endosome / signaling receptor activity / transcription by RNA polymerase II / cell differentiation / positive regulation of protein phosphorylation / 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 / mitochondrion / zinc ion binding / 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 (UBA) domain / Ubiquitin associated domain / Zinc finger ZZ-type signature. ...Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / UBA domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / 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 speciesMus musculus (house mouse)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, DGSA-DISTANCE GEOMETRY SIMULATE ANNEALING
Model detailslowest energy, model 1
AuthorsIsogai, S. / Morimoto, D. / Arita, K. / Unzai, S. / Tenno, T. / Hasegawa, J. / Sou, Y. / Komatsu, M. / Tanaka, K. / Shirakawa, M. / Tochio, H.
CitationJournal: To be Published
Title: Crystal structure of the UBA omain of p62 and its interaction with ubiquitin
Authors: Isogai, S. / Morimoto, D. / Arita, K. / Unzai, S. / Tenno, T. / Sou, Y. / Komatsu, M. / Tanaka, K. / Shirakawa, M. / Tochio, H.
History
DepositionJun 9, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)5,8181
Polymers5,8181
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100STRUCTURES WITH THE LOWEST ENER
RepresentativeModel #1lowest energy

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Components

#1: Protein Sequestosome-1 / STONE14 / Ubiquitin-binding protein p62


Mass: 5817.500 Da / Num. of mol.: 1 / Fragment: UBA domain (UNP RESIDUES 393-438)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: SQSTM1, A170, STAP / Production host: Escherichia coli (E. coli) / References: UniProt: Q64337

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D HBHA(CO)NH
1713D H(CCO)N 3D C(CO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D HN(CA)CO

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Sample preparation

DetailsContents: 0.4 mM [U-95% 13C; U-95% 15N] P62/SEQUESTOSOME-1-1, 2.4 mM Ubiquitin-2, 10 % [U-2H] D2O-3, 20 mM potassium phosphate-4, 5 mM potassium chloride-5, 1 mM EDTA-6, 10 % D2O-7, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMP62/SEQUESTOSOME-1-1[U-95% 13C; U-95% 15N]1
2.4 mMUbiquitin-21
10 %D2O-3[U-2H]1
20 mMpotassium phosphate-41
5 mMpotassium chloride-51
1 mMEDTA-61
10 %D2O-71
Sample conditionsIonic strength: 0.025 / pH: 6.8 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: BRUKER AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1GUNTERT, MUMENTHALERrefinement
CYANA2.1GUNTERT, MUMENTHALERstructure solution
Sparky3.113Goddarddata analysis
Sparky3.113Goddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
CANDIDHerrmann, Guntert and Wuthrichchemical shift assignment
ATNOSHerrmann and Wuthrichpeak picking
CARAKeller and Wuthrichchemical shift assignment
RefinementMethod: DGSA-distance geometry simulated annealing, DGSA-DISTANCE GEOMETRY SIMULATE ANNEALING
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LOWEST ENER
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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