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- PDB-6vti: Solution NMR structure of the N-terminal domain of the Serine/thr... -

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Basic information

Entry
Database: PDB / ID: 6vti
TitleSolution NMR structure of the N-terminal domain of the Serine/threonine-protein phosphatase 1 regulatory subunit 10, PPP1R10
ComponentsSerine/threonine-protein phosphatase 1 regulatory subunit 10
KeywordsNUCLEAR PROTEIN / PP1-PNUTS phosphatase complex / Regulatory Subunit / c-MYC oncoprotein
Function / homology
Function and homology information


negative regulation of mitotic DNA damage checkpoint / PTW/PP1 phosphatase complex / protein phosphatase 1 binding / positive regulation of telomere maintenance / protein phosphatase inhibitor activity / negative regulation of cardiac muscle cell apoptotic process / chromosome, telomeric region / nuclear body / chromatin / DNA binding ...negative regulation of mitotic DNA damage checkpoint / PTW/PP1 phosphatase complex / protein phosphatase 1 binding / positive regulation of telomere maintenance / protein phosphatase inhibitor activity / negative regulation of cardiac muscle cell apoptotic process / chromosome, telomeric region / nuclear body / chromatin / DNA binding / RNA binding / metal ion binding
Similarity search - Function
Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / TFIIS helical bundle-like domain / Transcription factor IIS, N-terminal / TFIIS N-terminal domain profile. / Zinc finger, CCCH-type superfamily / zinc finger / TFIIS/LEDGF domain superfamily / Zinc finger, CCCH-type / Zinc finger C3H1-type profile.
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 1 regulatory subunit 10
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / molecular dynamics
AuthorsLemak, A. / Wei, Y. / Duan, S. / Houliston, S. / Penn, L.Z. / Arrowsmith, C.H.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2015-05939 Canada
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: The MYC oncoprotein directly interacts with its chromatin cofactor PNUTS to recruit PP1 phosphatase.
Authors: Wei, Y. / Redel, C. / Ahlner, A. / Lemak, A. / Johansson-Akhe, I. / Houliston, S. / Kenney, T.M.G. / Tamachi, A. / Morad, V. / Duan, S. / Andrews, D.W. / Wallner, B. / Sunnerhagen, M. / ...Authors: Wei, Y. / Redel, C. / Ahlner, A. / Lemak, A. / Johansson-Akhe, I. / Houliston, S. / Kenney, T.M.G. / Tamachi, A. / Morad, V. / Duan, S. / Andrews, D.W. / Wallner, B. / Sunnerhagen, M. / Arrowsmith, C.H. / Penn, L.Z.
History
DepositionFeb 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 1 regulatory subunit 10


Theoretical massNumber of molelcules
Total (without water)16,6481
Polymers16,6481
Non-polymers00
Water00
1


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

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Components

#1: Protein Serine/threonine-protein phosphatase 1 regulatory subunit 10 / MHC class I region proline-rich protein CAT53 / Phosphatase 1 nuclear targeting subunit / Protein PNUTS


Mass: 16648.477 Da / Num. of mol.: 1 / Fragment: N-terminal domain residues 1-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ppp1r10, Cat53, Pnuts / Production host: Escherichia coli (E. coli) / References: UniProt: O55000

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic23D HN(CO)CA
141isotropic23D HNCA
151isotropic23D CBCA(CO)NH
161isotropic23D HBHA(CO)NH
181isotropic23D HNCO
171isotropic13D 1H-15N NOESY
191isotropic13D 1H-13C NOESY aliphatic
1101isotropic12D 1H-13C HSQC aromatic

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Sample preparation

DetailsType: solution
Contents: 450 uM [U-13C; U-15N] PPP1R10 N-terminal domain, 2.5 % glycerol, 200 mM NaCl, 20 mM HEPES, 1 mM DTT, 95% H2O/5% D2O
Details: Buffered protein - pH 6.9 / Label: Double labeled protein / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
450 uMPPP1R10 N-terminal domain[U-13C; U-15N]1
2.5 %glycerolnatural abundance1
200 mMNaClnatural abundance1
20 mMHEPESnatural abundance1
1 mMDTTnatural abundance1
Sample conditionsIonic strength: 200 mM / Label: conditions_1 / pH: 6.9 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II8001
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
ABACUSLemak and Arrowsmithchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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