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- PDB-6lqz: Solution structure of Taf14ET-Sth1EBMC -

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Basic information

Entry
Database: PDB / ID: 6lqz
TitleSolution structure of Taf14ET-Sth1EBMC
Components
  • Nuclear protein STH1/NPS1
  • Transcription initiation factor TFIID subunit 14
KeywordsTRANSCRIPTION / protein interaction module / phase separation
Function / homology
Function and homology information


NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / chromatin remodeling at centromere / DNA translocase activity / nucleosome disassembly / Ino80 complex / mediator complex / RSC-type complex / transcription factor TFIIF complex ...NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / chromatin remodeling at centromere / DNA translocase activity / nucleosome disassembly / Ino80 complex / mediator complex / RSC-type complex / transcription factor TFIIF complex / SWI/SNF complex / ATP-dependent chromatin remodeler activity / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / chromosome, centromeric region / ATP-dependent activity, acting on DNA / RNA polymerase II preinitiation complex assembly / cytoskeleton organization / meiotic cell cycle / helicase activity / chromosome segregation / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / base-excision repair / lysine-acetylated histone binding / double-strand break repair / histone binding / DNA helicase / transcription by RNA polymerase II / chromatin remodeling / DNA repair / DNA-templated transcription / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / nucleus
Similarity search - Function
SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain ...SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / NET domain / Bromodomain extra-terminal - transcription regulation / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / helicase superfamily c-terminal domain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Nuclear protein STH1/NPS1 / Transcription initiation factor TFIID subunit 14
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsWu, B. / Chen, G. / Chen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670748 China
CitationJournal: Nat Commun / Year: 2020
Title: Taf14 recognizes a common motif in transcriptional machineries and facilitates their clustering by phase separation.
Authors: Chen, G. / Wang, D. / Wu, B. / Yan, F. / Xue, H. / Wang, Q. / Quan, S. / Chen, Y.
History
DepositionJan 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 14
B: Nuclear protein STH1/NPS1


Theoretical massNumber of molelcules
Total (without water)14,7012
Polymers14,7012
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1610 Å2
ΔGint-11 kcal/mol
Surface area11070 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcription initiation factor TFIID subunit 14 / Actin non-complementing mutant 1 / Chromosome stability protein 10 / SWI/SNF chromatin-remodeling ...Actin non-complementing mutant 1 / Chromosome stability protein 10 / SWI/SNF chromatin-remodeling complex subunit TAF14 / SWI/SNF complex 29 kDa subunit / SWI/SNF complex subunit TAF14 / TBP-associated factor 14 / TBP-associated factor 30 kDa / Transcription factor G 30 kDa subunit / Transcription initiation factor TFIIF 30 kDa subunit


Mass: 8083.089 Da / Num. of mol.: 1 / Fragment: Taf14ET
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TAF14, ANC1, CST10, SWP29, TAF30, TFG3, YPL129W / Production host: Escherichia coli (E. coli) / References: UniProt: P35189
#2: Protein Nuclear protein STH1/NPS1 / ATP-dependent helicase STH1 / Chromatin structure-remodeling complex protein STH1 / SNF2 homolog


Mass: 6617.640 Da / Num. of mol.: 1 / Fragment: Sth1EBMC
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: STH1, NPS1, YIL126W / Production host: Escherichia coli (E. coli) / References: UniProt: P32597, DNA helicase

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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
131isotropic12D 1H-13C HSQC aromatic
141isotropic23D HNCO
151isotropic23D HN(CA)CO
161isotropic23D HN(CO)CA
1121isotropic23D HNCA
1111isotropic23D CBCA(CO)NH
1101isotropic23D HN(CA)CB
191isotropic23D CBCA(CO)NH
181isotropic23D HBHA(CO)NH
171isotropic23D HNHA
1161isotropic13D (H)CCH-TOCSY
1151isotropic13D CCH-TOCSY
1141isotropic13D 1H-15N NOESY
1131isotropic13D 1H-13C NOESY aliphatic
1171isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-100% 13C; U-100% 15N] Taf14ET, 1.5 mM [U-100% 13C; U-100% 15N] Sth1EBMC, 20 mM Phosphate buffer, 100 mM sodium chloride, 1 % v/v inhabitor cocktail, 0.04 % sodium azide, 90% H2O/10% D2O
Details: 15N/13C-labeled Taf14ET and 15N/13C-labeled Sth1EBMC
Label: 15N/13C_labeled / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTaf14ET[U-100% 13C; U-100% 15N]1
1.5 mMSth1EBMC[U-100% 13C; U-100% 15N]1
20 mMPhosphate buffernatural abundance1
100 mMsodium chloridenatural abundance1
1 % v/vinhabitor cocktailnatural abundance1
0.04 %sodium azidenatural abundance1
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent DD2AgilentDD28001
Agilent DD2AgilentDD26002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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