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- PDB-6zv2: TFIIS N-terminal domain (TND) from human PPP1R10 -

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Basic information

Entry
Database: PDB / ID: 6zv2
TitleTFIIS N-terminal domain (TND) from human PPP1R10
ComponentsSerine/threonine-protein phosphatase 1 regulatory subunit 10
KeywordsTRANSCRIPTION / transcription elongation
Function / homology
Function and homology information


negative regulation of mitotic DNA damage checkpoint / PTW/PP1 phosphatase complex / protein phosphatase 1 binding / negative regulation of cardiac muscle cell apoptotic process / protein phosphatase inhibitor activity / positive regulation of telomere maintenance / protein import into nucleus / nuclear body / chromatin / DNA binding ...negative regulation of mitotic DNA damage checkpoint / PTW/PP1 phosphatase complex / protein phosphatase 1 binding / negative regulation of cardiac muscle cell apoptotic process / protein phosphatase inhibitor activity / positive regulation of telomere maintenance / protein import into nucleus / nuclear body / chromatin / DNA binding / RNA binding / nucleoplasm / metal ion binding / nucleus
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 N-terminal domain profile. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / TFIIS/LEDGF domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 1 regulatory subunit 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics / molecular dynamics
AuthorsVeverka, V.
CitationJournal: Science / Year: 2021
Title: A ubiquitous disordered protein interaction module orchestrates transcription elongation.
Authors: Cermakova, K. / Demeulemeester, J. / Lux, V. / Nedomova, M. / Goldman, S.R. / Smith, E.A. / Srb, P. / Hexnerova, R. / Fabry, M. / Madlikova, M. / Horejsi, M. / De Rijck, J. / Debyser, Z. / ...Authors: Cermakova, K. / Demeulemeester, J. / Lux, V. / Nedomova, M. / Goldman, S.R. / Smith, E.A. / Srb, P. / Hexnerova, R. / Fabry, M. / Madlikova, M. / Horejsi, M. / De Rijck, J. / Debyser, Z. / Adelman, K. / Hodges, H.C. / Veverka, V.
History
DepositionJul 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 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)17,2221
Polymers17,2221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9210 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 100structures with the least restraint violations
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 / PP1-binding protein of 114 kDa / Phosphatase 1 ...MHC class I region proline-rich protein CAT53 / PP1-binding protein of 114 kDa / Phosphatase 1 nuclear targeting subunit / Protein FB19 / p99


Mass: 17221.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1R10, CAT53, FB19, PNUTS / Production host: Escherichia coli (E. coli) / References: UniProt: Q96QC0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC
121isotropic12D 1H-15N HSQC
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
171isotropic13D HBHA(CO)NH
161isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.7 mM [U-13C; U-15N] PPP1R10, 25 mM [U-2H] TRIS, 200 mM sodium chloride, 1 mM TCEP, 95% H2O/5% D2O
Label: s1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMPPP1R10[U-13C; U-15N]1
25 mMTRIS[U-2H]1
200 mMsodium chloridenatural abundance1
1 mMTCEPnatural abundance1
Sample conditionsIonic strength: 225 mM / Label: c1 / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
YASARAYASARArefinement
Refinement
MethodSoftware ordinal
torsion angle dynamics2
molecular dynamics3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 40

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