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- PDB-2ktr: NMR structure of p62 PB1 dimer determined based on PCS -

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Basic information

Entry
Database: PDB / ID: 2ktr
TitleNMR structure of p62 PB1 dimer determined based on PCS
Components(Sequestosome-1) x 2
KeywordsSignaling Protein / Transport Protein / Autophagy / NF-kB signaling / homo-oligomer / PB1 dimer
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 / PINK1-PRKN Mediated Mitophagy / KEAP1-NFE2L2 pathway / 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 / PINK1-PRKN Mediated Mitophagy / KEAP1-NFE2L2 pathway / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / protein targeting to vacuole involved in autophagy / Lewy body / response to mitochondrial depolarisation / aggrephagy / negative regulation of toll-like receptor 4 signaling pathway / amphisome / regulation of protein complex stability / endosome organization / pexophagy / membraneless organelle assembly / phagophore assembly site / ubiquitin-modified protein reader activity / regulation of canonical NF-kappaB signal transduction / aggresome / negative regulation of ferroptosis / intracellular membraneless organelle / K63-linked polyubiquitin modification-dependent protein binding / temperature homeostasis / cellular response to stress / autolysosome / molecular sequestering activity / immune system process / mitophagy / energy homeostasis / inclusion body / ionotropic glutamate receptor binding / positive regulation of autophagy / signaling adaptor activity / sperm midpiece / negative regulation of protein ubiquitination / SH2 domain binding / protein sequestering activity / autophagosome / sarcomere / protein kinase C binding / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / positive regulation of protein localization to plasma membrane / macroautophagy / P-body / molecular condensate scaffold activity / protein catabolic process / PML body / autophagy / protein import into nucleus / late endosome / signaling receptor activity / protein-macromolecule adaptor activity / transcription by RNA polymerase II / cell differentiation / apoptotic process / synapse / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / glutamatergic synapse / enzyme binding / negative regulation of transcription by RNA polymerase II / 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 / : / PB1 domain profile. / Ubiquitin associated domain ...Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / : / UBA domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / 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
TERBIUM(III) ION / Sequestosome-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsSaio, T. / Yokochi, M. / Kumeta, H. / Inagaki, F.
CitationJournal: J.Biomol.Nmr / Year: 2010
Title: PCS-based structure determination of protein-protein complexes
Authors: Saio, T. / Yokochi, M. / Kumeta, H. / Inagaki, F.
History
DepositionFeb 5, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / struct_ref_seq / 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.db_align_beg / _struct_ref_seq.db_align_end / _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
A: Sequestosome-1
B: Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3913
Polymers24,2322
Non-polymers1591
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area758.5 Å2
ΔGint5.2 kcal/mol
Surface area12301.2 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
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: 13074.684 Da / Num. of mol.: 1 / Fragment: PB1 domain, OPR domain, residues 3-100 / Mutation: C42S, D67A, D69R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: O08623
#2: Protein Sequestosome-1 / p62 / Ubiquitin-binding protein p62 / Protein kinase C-zeta-interacting protein / PKC-zeta-interacting protein


Mass: 11157.524 Da / Num. of mol.: 1 / Fragment: PB1 domain, OPR domain, residues 3-100 / Mutation: K207E, C226S, C242S, R294A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: O08623
#3: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Tb
Compound detailsA67, R69, E207, AND A294 ARE MUTATIONS FOR THE PREVENTION OF HOMO-OLIGOMERIZATION. S42, S226, AND ...A67, R69, E207, AND A294 ARE MUTATIONS FOR THE PREVENTION OF HOMO-OLIGOMERIZATION. S42, S226, AND S242 ARE FOR THE FIXATION OF LANTHANIDE-BINDING PEPTIDE TAG(LBT).
Sequence detailsTHE SEQUENCE CYVDTNNDGAYEGDELHMG OF CHAIN A IS FOR LANTHANIDE-BINDING PEPTIDE SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1312D 1H-13C HSQC
1422D 1H-13C HSQC
1513D HNCA
1623D HNCA
1713D HN(CO)CA
1823D HN(CO)CA
1913D HN(CA)CB
11023D HN(CA)CB
11113D HNCO
11223D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM [U-99% 13C; U-99% 15N] p62_1; 0.5mM p62_2; 20mM MES; 50mM sodium chloride; 0.5mM TERBIUM(III) ION; 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM p62_1; 0.5mM [U-99% 13C; U-99% 15N] p62_2; 20mM MES; 50mM sodium chloride; 0.5mM TERBIUM(III) ION; 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity_1-1[U-99% 13C; U-99% 15N]1
0.5 mMentity_2-21
20 mMMES-31
50 mMsodium chloride-41
0.5 mMTERBIUM(III) ION-51
0.5 mMentity_1-62
0.5 mMentity_2-7[U-99% 13C; U-99% 15N]2
20 mMMES-82
50 mMsodium chloride-92
0.5 mMTERBIUM(III) ION-102
Sample conditionsIonic strength: 0.05 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
OliviaMasashi Yokochidata analysis
OliviaMasashi Yokochichemical shift assignment
X-PLOR NIH2.9.20Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.9.20Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
Details: In this work, the dimer structure of p62 PB1 was determined by using a rigid-body docking calculation based on the pseudo-contact shift. In the docking calculation, the coordinates of chain ...Details: In this work, the dimer structure of p62 PB1 was determined by using a rigid-body docking calculation based on the pseudo-contact shift. In the docking calculation, the coordinates of chain A were held fixed, whereas the coordinates of chain B were treated as a rigid body and set free to rotate and translate. The differences among the models are relative orientations between chain A and chain B, not each coordinates. In the calculation, monomer structures of DR and KE were docked each other based on the inter-subunit restraints from pseudo-contact shifts. The coordinates of DR and KE were generated from the monomer structure of DR (2kkc), using PyMOL software. For pseudo-contact shift restraints, we need a paramagnetic lanthanide ion fixed in the target protein. To fix a lanthanide ions to DR, we utilized the lanthanide binding peptide tag (LBT).The chain A represents LBT-DR, and chain B does KE. We collected the pseudo-contact shift restrains using LBT-DR/KE complex, while the docking calculations were performed using the coordinates without LBT.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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