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- PDB-2n23: NMR structure of the complex between the PH domain of the Tfb1 su... -

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Basic information

Entry
Database: PDB / ID: 2n23
TitleNMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the N-terminal activation domain of EKLF (TAD1)
Components
  • Krueppel-like factor 1
  • RNA polymerase II transcription factor B subunit 1
KeywordsTRANSCRIPTION / Transcription factor TFIIH / Transactivation domain / Erythroid Kr ppel-like factor 1 / Transcriptional activation / p62/Tfb1 subunit
Function / homology
Function and homology information


cellular response to peptide / phosphatidylinositol-5-phosphate binding / nucleotide-excision repair factor 3 complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex ...cellular response to peptide / phosphatidylinositol-5-phosphate binding / nucleotide-excision repair factor 3 complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / maternal process involved in female pregnancy / transcription by RNA polymerase I / erythrocyte differentiation / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / transcription by RNA polymerase II / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA repair / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
Krueppel-like factor 1, transactivation domain 2 / Krueppel-like factor 1, transactivation domain 1 / Erythroid krueppel-like transcription factor, transactivation 1 / Erythroid krueppel-like transcription factor, transactivation 2 / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain ...Krueppel-like factor 1, transactivation domain 2 / Krueppel-like factor 1, transactivation domain 1 / Erythroid krueppel-like transcription factor, transactivation 1 / Erythroid krueppel-like transcription factor, transactivation 2 / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / Zinc finger, C2H2 type / PH-domain like / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
General transcription and DNA repair factor IIH subunit TFB1 / Krueppel-like factor 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
Homo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsLecoq, L. / Morse, T. / Raiola, L. / Arseneault, G. / Omichinski, J.
CitationJournal: To be Published
Title: Structural Characterization of the Complex between the N-terminal Transactivation Domain of EKLF and the p62/Tfb1 subunit of TFIIH
Authors: Morse, T. / Lecoq, L. / Raiola, L. / Arseneault, G. / Omichinski, J.
History
DepositionApr 27, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase II transcription factor B subunit 1
B: Krueppel-like factor 1


Theoretical massNumber of molelcules
Total (without water)15,2632
Polymers15,2632
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 260structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA polymerase II transcription factor B subunit 1 / General transcription and DNA repair factor IIH subunit TFB1 / TFIIH subunit TFB1 / RNA polymerase ...General transcription and DNA repair factor IIH subunit TFB1 / TFIIH subunit TFB1 / RNA polymerase II transcription factor B 73 kDa subunit / RNA polymerase II transcription factor B p73 subunit


Mass: 12903.701 Da / Num. of mol.: 1 / Fragment: Pleckstrin homology domain, UNP residues 2-115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: TFB1, YDR311W, D9740.3 / Production host: Escherichia coli (E. coli) / References: UniProt: P32776
#2: Protein/peptide Krueppel-like factor 1 / Erythroid krueppel-like transcription factor / EKLF


Mass: 2359.483 Da / Num. of mol.: 1 / Fragment: Transactivation Domain 1, UNP residues 22-40
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLF1, EKLF / Production host: Escherichia coli (E. coli) / References: UniProt: Q13351

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D (H)CCH-TOCSY
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D 1H-15N NOESY
1722D 1H-13C HSQC
1823D 1H-13C NOESY
1923D intermolecular NOESY
11032D 1H-15N HSQC
11133D (H)CCH-TOCSY
11233D CBCA(CO)NH
11333D HN(CA)CB
11433D 1H-15N NOESY
11542D 1H-13C HSQC aliphatic
11642D 1H-13C HSQC aromatic
11743D 1H-13C NOESY aliphatic
11843D 1H-13C NOESY aromatic
11943D intermolecular NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 13C; U-100% 15N] RNA polymerase II transcription factor B subunit 1, 2 mM N-terminal transactivation domain of Krueppel-like factor 1, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-100% 13C; U-100% 15N] RNA polymerase II transcription factor B subunit 1, 2 mM N-terminal transactivation domain of Krueppel-like factor 1, 100% D2O100% D2O
30.8 mM [U-100% 13C; U-100% 15N] N-terminal transactivation domain of Krueppel-like factor 1, 2 mM RNA polymerase II transcription factor B subunit 1, 90% H2O/10% D2O90% H2O/10% D2O
40.8 mM [U-100% 13C; U-100% 15N] N-terminal transactivation domain of Krueppel-like factor 1, 2 mM RNA polymerase II transcription factor B subunit 1, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMRNA polymerase II transcription factor B subunit 1-1[U-100% 13C; U-100% 15N]1
2 mMN-terminal transactivation domain of Krueppel-like factor 1-21
0.8 mMRNA polymerase II transcription factor B subunit 1-3[U-100% 13C; U-100% 15N]2
2 mMN-terminal transactivation domain of Krueppel-like factor 1-42
0.8 mMN-terminal transactivation domain of Krueppel-like factor 1-5[U-100% 13C; U-100% 15N]3
2 mMRNA polymerase II transcription factor B subunit 1-63
0.8 mMN-terminal transactivation domain of Krueppel-like factor 1-7[U-100% 13C; U-100% 15N]4
2 mMRNA polymerase II transcription factor B subunit 1-84
Sample conditionsIonic strength: 0 / pH: 6.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

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Processing

NMR softwareName: CNS / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2737 / NOE intraresidue total count: 1453 / NOE long range total count: 540 / NOE medium range total count: 2015 / NOE sequential total count: 486 / Protein phi angle constraints total count: 119 / Protein psi angle constraints total count: 119
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 260 / Conformers submitted total number: 20

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