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- PDB-7lqt: Solution NMR structure of the PNUTS amino-terminal Domain fused t... -

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Basic information

Entry
Database: PDB / ID: 7lqt
TitleSolution NMR structure of the PNUTS amino-terminal Domain fused to Myc Homology Box 0
ComponentsSerine/threonine-protein phosphatase 1 regulatory subunit 10,Myc proto-oncogene protein fusion
KeywordsNUCLEAR PROTEIN / PP1-PNUTS phosphatase complex / Regulatory Subunit / c-MYC oncoprotein / Myc Box 0
Function / homology
Function and homology information


pyruvate transport / cellular response to arsenite(3-) / cellular response to dimethyl sulfoxide / TFAP2 (AP-2) family regulates transcription of cell cycle factors / canonical Wnt signaling pathway involved in positive regulation of apoptotic process / : / canonical Wnt signaling pathway involved in negative regulation of apoptotic process / negative regulation of mitotic DNA damage checkpoint / cellular response to putrescine / : ...pyruvate transport / cellular response to arsenite(3-) / cellular response to dimethyl sulfoxide / TFAP2 (AP-2) family regulates transcription of cell cycle factors / canonical Wnt signaling pathway involved in positive regulation of apoptotic process / : / canonical Wnt signaling pathway involved in negative regulation of apoptotic process / negative regulation of mitotic DNA damage checkpoint / cellular response to putrescine / : / Estrogen-dependent gene expression / cellular response to growth hormone stimulus / cellular response to cycloheximide / lactic acid secretion / fungal-type cell wall polysaccharide metabolic process / re-entry into mitotic cell cycle / positive regulation of metanephric cap mesenchymal cell proliferation / cellular response to endothelin / ovulation / cellular response to xenobiotic stimulus => GO:0071466 / inner mitochondrial membrane organization / : / cellular response to interferon-alpha / flavonoid metabolic process / response to human chorionic gonadotropin / positive regulation of B cell apoptotic process / regulation of somatic stem cell population maintenance / positive regulation of cellular respiration / PTW/PP1 phosphatase complex / cellular response to prolactin / cellular response to carbohydrate stimulus / Ub-specific processing proteases / cellular response to lectin / response to xenobiotic stimulus => GO:0009410 / G0 to G1 transition / detection of mechanical stimulus involved in sensory perception of sound / negative regulation of cell division / protein phosphatase 1 binding / negative regulation of monocyte differentiation / cellular response to phorbol 13-acetate 12-myristate / cellular response to hydrostatic pressure / positive regulation of telomere maintenance / B cell apoptotic process / regulation of oxidative phosphorylation / cellular response to testosterone stimulus / positive regulation of oxidative phosphorylation / negative regulation of glucose import / response to alkaloid / cellular response to fibroblast growth factor stimulus / cellular response to angiotensin / middle ear morphogenesis / positive regulation of mitochondrial membrane potential / skeletal system morphogenesis / regulation of telomere maintenance / positive regulation of mesenchymal cell proliferation / protein-DNA complex disassembly / protein phosphatase inhibitor activity / negative regulation of cardiac muscle cell apoptotic process / branching involved in ureteric bud morphogenesis / amino acid transport / hypothalamus development / pigmentation / positive regulation of DNA biosynthetic process / positive regulation of ATP biosynthetic process / cellular response to platelet-derived growth factor stimulus / positive regulation of catalytic activity / positive regulation of smooth muscle cell migration / transformation of host cell by virus / E-box binding / skeletal muscle cell differentiation / cellular response to cytokine stimulus / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / cellular response to organic cyclic compound / chromosome organization / positive regulation of transcription initiation by RNA polymerase II / positive regulation of DNA binding / cellular response to interleukin-1 / cellular response to estrogen stimulus / cis-regulatory region sequence-specific DNA binding / positive regulation of cell cycle / cellular response to retinoic acid / core promoter sequence-specific DNA binding / negative regulation of fibroblast proliferation / ovarian follicle development / positive regulation of glial cell proliferation / : / cellular response to epidermal growth factor stimulus / regulation of mitotic cell cycle / ERK1 and ERK2 cascade / positive regulation of glycolytic process / negative regulation of protein binding / DNA-templated transcription initiation / positive regulation of epithelial cell proliferation / liver regeneration / response to gamma radiation / positive regulation of apoptotic signaling pathway / positive regulation of smooth muscle cell proliferation / euchromatin / response to radiation / protein processing
Similarity search - Function
Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / Myc amino-terminal region / 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 ...Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / Myc amino-terminal region / 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 / Helix-loop-helix DNA-binding domain / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile.
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 1 regulatory subunit 10 / Myc proto-oncogene protein
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.
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 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 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,Myc proto-oncogene protein fusion


Theoretical massNumber of molelcules
Total (without water)19,3911
Polymers19,3911
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
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,Myc proto-oncogene protein fusion / MHC class I region proline-rich protein CAT53 / Phosphatase 1 nuclear targeting subunit / Protein ...MHC class I region proline-rich protein CAT53 / Phosphatase 1 nuclear targeting subunit / Protein PNUTS / Proto-oncogene c-Myc / Transcription factor p64


Mass: 19391.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ppp1r10, Cat53, Pnuts, Myc / Production host: Escherichia coli (E. coli) / References: UniProt: O55000, UniProt: P09416

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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
171isotropic22D 1H-13C HSQC aliphatic
161isotropic22D 1H-13C HSQC aromatic
121isotropic13D HN(CO)CA
131isotropic13D HNCA
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
1101isotropic13D HBHA(CO)NH
191isotropic13D HN(CA)CO
181isotropic23D 1H-15N NOESY
1121isotropic23D 1H-13C NOESY aliphatic
1111isotropic23D 1H-13C NOESY aromatic
1131isotropic23D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 5 % glycerol, 400 uM [U-100% 13C; U-100% 15N] labeled protein, 95% H2O/5% D2O
Details: Buffered protein solution / Label: labeled protein / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMHEPESnatural abundance1
200 mMsodium chloridenatural abundance1
2 mMDTTnatural abundance1
5 %glycerolnatural abundance1
400 uMlabeled protein[U-100% 13C; U-100% 15N]1
Sample conditionsDetails: 400 uM protein in a 3 mM tube / Ionic 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 IIIBrukerAVANCE III6001
Bruker AVANCE IIBrukerAVANCE II8002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
FMCGUIA. Lemak & C.H. 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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