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- PDB-2l2i: NMR Structure of the complex between the Tfb1 subunit of TFIIH an... -

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Basic information

Entry
Database: PDB / ID: 2l2i
TitleNMR Structure of the complex between the Tfb1 subunit of TFIIH and the activation domain of EKLF
Components
  • Krueppel-like factor 1
  • RNA polymerase II transcription factor B subunit 1
KeywordsTRANSCRIPTION / Transcription Factor TFIIH / Erythroid Kruppel-Like Factor EKLF / Activator / Protein Structure / Mutation / Gene Expression Regulation
Function / homology
Function and homology information


phosphatidylinositol-5-phosphate binding / cellular response to peptide / 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 ...phosphatidylinositol-5-phosphate binding / cellular response to peptide / 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 / simulated annealing
Model detailslowest energy, model 1
AuthorsMas, C. / Di Lello, P. / Lafrance-Vanasse, J. / Omichinski, J.G.
CitationJournal: To be Published
Title: NMR Structure of the complex between the Tfb1 subunit of TFIIH and the activation domain of EKLF
Authors: Mas, C. / Lussier-Price, M. / Morse, T. / Arsenault, G. / Di Lello, P. / Soni, S. / Lafrance-Vanasse, J. / Bieker, J.J. / Omichinski, J.G.
History
DepositionAug 18, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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)17,3622
Polymers17,3622
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 / 100structures 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: PH 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: D9740.3, TFB1, YDR311W / Plasmid: pGEX-2TK / Production host: Escherichia coli (E. coli) / Strain (production host): Topp2 / References: UniProt: P32776
#2: Protein/peptide Krueppel-like factor 1 / Erythroid krueppel-like transcription factor / EKLF


Mass: 4458.609 Da / Num. of mol.: 1 / Fragment: Transactivation Domain (UNP residues 51-90)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EKLF, KLF1 / Plasmid: pGEX-2TK / Production host: Escherichia coli (E. coli) / Strain (production host): Topp2 / 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
1232D 1H-15N HSQC
1362D 1H-13C HSQC
1442D 1H-13C HSQC
1523D HNCO
1653D HNCO
1723D HN(CA)CB
1853D HN(CA)CB
1923D HBHA(CO)NH
11053D HBHA(CO)NH
11163D (H)CCH-TOCSY
11243D (H)CCH-TOCSY
11363D (H)CCH-COSY
11443D (H)CCH-COSY
11513D 1H-15N NOESY
11633D 1H-15N NOESY
11763D 1H-13C NOESY
11843D 1H-13C NOESY
11963D 15N-13C-FILTERED-NOESY
12043D 15N-13C-FILTERED-NOESY
12123D CCC-TOCSY
12253D CCC-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] Tfb1, 2 mM EKLF, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] Tfb1, 2 mM EKLF, 90% H2O/10% D2O90% H2O/10% D2O
30.6 mM [U-100% 15N] EKLF, 1.2 mM Tfb1, 90% H2O/10% D2O90% H2O/10% D2O
40.6 mM [U-100% 13C; U-100% 15N] EKLF, 1.2 mM Tfb1, 100% D2O100% D2O
50.6 mM [U-100% 13C; U-100% 15N] EKLF, 1.2 mM Tfb1, 90% H2O/10% D2O90% H2O/10% D2O
61 mM [U-100% 13C; U-100% 15N] Tfb1, 2 mM EKLF, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTfb1-1[U-100% 15N]1
2 mMEKLF-21
1 mMTfb1-3[U-100% 13C; U-100% 15N]2
2 mMEKLF-42
0.6 mMEKLF-5[U-100% 15N]3
1.2 mMTfb1-63
0.6 mMEKLF-7[U-100% 13C; U-100% 15N]4
1.2 mMTfb1-84
0.6 mMEKLF-9[U-100% 13C; U-100% 15N]5
1.2 mMTfb1-105
1 mMTfb1-11[U-100% 13C; U-100% 15N]6
2 mMEKLF-126
Sample conditionsIonic strength: 20mM Sodium Phosphate / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityVarianUNITY5001
Varian UnityVarianUNITY6002
Varian UnityVarianUNITY8003

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxchemical shift calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
ProcheckNMRLaskowski and MacArthurdata analysis
AQUARullmann, Doreleijers and Kapteindata analysis
VNMRVariancollection
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / 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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