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- PDB-6qtc: tSH2 domain of transcription elongation factor Spt6 complexed wit... -

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Basic information

Entry
Database: PDB / ID: 6qtc
TitletSH2 domain of transcription elongation factor Spt6 complexed with tyrosine phosphorylated CTD
Components
  • Tyrosine phosphorylated CTD
  • tSH2 domain of transcription elongation factor Spt6
KeywordsGENE REGULATION / CTD / elongation factor / RNA polymerase II / tandem SH2 domain
Function / homology
Function and homology information


carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / regulation of transcriptional start site selection at RNA polymerase II promoter / transcription antitermination factor activity, DNA binding / regulation of mRNA 3'-end processing / transcription elongation-coupled chromatin remodeling / poly(A)+ mRNA export from nucleus / nucleosome binding / transcription elongation factor complex / positive regulation of transcription elongation by RNA polymerase II / euchromatin ...carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / regulation of transcriptional start site selection at RNA polymerase II promoter / transcription antitermination factor activity, DNA binding / regulation of mRNA 3'-end processing / transcription elongation-coupled chromatin remodeling / poly(A)+ mRNA export from nucleus / nucleosome binding / transcription elongation factor complex / positive regulation of transcription elongation by RNA polymerase II / euchromatin / nucleosome assembly / histone binding / negative regulation of transcription by RNA polymerase II / DNA binding
Similarity search - Function
: / Spt6, S1/OB domain / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif / Spt6, SH2 domain, C terminus / Acidic N-terminal SPT6 ...: / Spt6, S1/OB domain / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif / Spt6, SH2 domain, C terminus / Acidic N-terminal SPT6 / Helix-hairpin-helix motif / Holliday-junction resolvase-like of SPT6 / Helix-turn-helix DNA-binding domain of SPT6 / Tex-like protein, HTH domain superfamily / Tex-like domain superfamily / Spt6, Death-like domain / Transcription elongation factor Spt6 / Spt6, SH2 domain, N terminus / Spt6, SH2 domain / SH2 domain / YqgF/RNase H-like domain superfamily / RuvA domain 2-like / SH2 domain / SHC Adaptor Protein / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcription elongation factor SPT6
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodSOLUTION NMR / simulated annealing
AuthorsBrazda, P. / Krejcikova, M. / Smirakova, E. / Kubicek, K. / Stefl, R.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Grant Agency of the Czech RepublicGA15-24117S Czech Republic
CitationJournal: To Be Published
Title: tSH2 domain of transcription elongation factor Spt6 complexed with tyrosine phosphorylated CTD
Authors: Brazda, P. / Krejcikova, M. / Kasiliauskaite, A. / Smirakova, E. / Klumpler, T. / Vacha, R. / Kubicek, K. / Stefl, R.
History
DepositionFeb 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 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
Revision 1.2Nov 15, 2023Group: 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: tSH2 domain of transcription elongation factor Spt6
B: Tyrosine phosphorylated CTD


Theoretical massNumber of molelcules
Total (without water)25,0592
Polymers25,0592
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1880 Å2
ΔGint-18 kcal/mol
Surface area10690 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein tSH2 domain of transcription elongation factor Spt6


Mass: 23257.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Variant: wt / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / References: UniProt: Q6FLB1
#2: Protein/peptide Tyrosine phosphorylated CTD


Mass: 1801.647 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Candida glabrata (fungus)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
122isotropic13D HN(CO)CA
132isotropic13D CBCA(CO)NH
142isotropic13D HN(CA)CB
152isotropic23D (H)CCH-TOCSY
162isotropic33D 1H-13C NOESY aliphatic
171isotropic33D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-99% 15N] spt6, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.5 mM [U-99% 13C; U-99% 15N] spt6, 90% H2O/10% D2O13C15N_sample90% H2O/10% D2O
solution30.5 mM spt6, 90% H2O/10% D2Ounlbl_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMspt6[U-99% 15N]1
0.5 mMspt6[U-99% 13C; U-99% 15N]2
0.5 mMspt6natural abundance3
Sample conditionsIonic strength: 10 mM / Label: conditions_1 / pH: 7 / PH err: 0.1 / Pressure: 1 Pa / Temperature: 310 K / Temperature err: 0.05

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III7001cryoprobe
Bruker AVANCE IIIBrukerAVANCE III8502cryoprobe
Bruker AVANCE IIIBrukerAVANCE III9503cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.115Goddardchemical shift assignment
CYANA3.97-3.98.5Guntert, Mumenthaler and Wuthrichstructure calculation
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
TopSpin3.5Bruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: NMR refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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