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- PDB-2kkc: NMR structure of the p62 PB1 domain -

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Basic information

Entry
Database: PDB / ID: 2kkc
TitleNMR structure of the p62 PB1 domain
ComponentsSequestosome-1
KeywordsSIGNALING PROTEIN / TRANSPORT PROTEIN / p62 / PB1 / autophagy / ubiquitin-proteasome system / NF-kB signaling / Alternative splicing / Apoptosis / Cytoplasm / Differentiation / Endosome / Immune response / Metal-binding / Nucleus / Phosphoprotein / Zinc / Zinc-finger
Function / homology
Function and homology information


Interleukin-1 signaling / Pexophagy / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / p75NTR recruits signalling complexes / KEAP1-NFE2L2 pathway / PINK1-PRKN Mediated Mitophagy / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / protein targeting to vacuole involved in autophagy ...Interleukin-1 signaling / Pexophagy / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / p75NTR recruits signalling complexes / KEAP1-NFE2L2 pathway / PINK1-PRKN Mediated Mitophagy / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / protein targeting to vacuole involved in autophagy / Lewy body / negative regulation of toll-like receptor 4 signaling pathway / non-membrane-bounded organelle assembly / aggrephagy / response to mitochondrial depolarisation / amphisome / 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 / 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 / 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 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. / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsYokochi, M. / Inagaki, F.
CitationJournal: J.Biomol.Nmr / Year: 2009
Title: The NMR structure of the p62 PB1 domain, a key protein in autophagy and NF-kappaB signaling pathway
Authors: Saio, T. / Yokochi, M. / Inagaki, F.
History
DepositionJun 18, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _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)11,4281
Polymers11,4281
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Sequestosome-1 / p62 / Ubiquitin-binding protein p62 / Protein kinase C-zeta-interacting protein / PKC-zeta-interacting protein


Mass: 11428.100 Da / Num. of mol.: 1 / Fragment: PB1 domain, OPR domain, residues 3-100 / Mutation: D67A, D69R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O08623

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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 HNCO
1513D HNCA
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D HN(CO)CA
1913D (H)CCH-TOCSY
11013D (H)CCH-TOCSY
11113D HNCAHA
11213D 1H-15N NOESY
11313D 1H-13C NOESY

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Sample preparation

DetailsContents: 1mM [U-99% 13C; U-99% 15N] p62 PB1-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: p62 PB1-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Unity Inova / Manufacturer: Varian / Model: Unity Inova / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Olivia1.15.2Masashi Yokochichemical shift assignment
Olivia1.15.2Masashi Yokochidata analysis
Olivia1.15.2Masashi Yokochipeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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