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- PDB-2m14: NMR structure of the complex between the PH domain of the Tfb1 su... -

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Basic information

Entry
Database: PDB / ID: 2m14
TitleNMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad4
Components
  • DNA repair protein RAD4
  • RNA polymerase II transcription factor B subunit 1
KeywordsTRANSCRIPTION/DNA BINDING PROTEIN / Tfb1 / PH domain / TRANSCRIPTION-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / XPC complex / nucleotide-excision repair, DNA damage recognition / phosphatidylinositol-5-phosphate binding / nucleotide-excision repair factor 3 complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / RNA Pol II CTD phosphorylation and interaction with CE ...nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / XPC complex / nucleotide-excision repair, DNA damage recognition / phosphatidylinositol-5-phosphate binding / nucleotide-excision repair factor 3 complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / 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 / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / DNA topological change / Dual incision in TC-NER / mismatch repair / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / single-stranded DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / damaged DNA binding / DNA repair / negative regulation of transcription by RNA polymerase II / nucleus / cytoplasm / cytosol
Similarity search - Function
DNA repair protein Rad4 / DNA repair protein Rad4, subgroup / Rad4/PNGase transglutaminase-like fold / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4, beta-hairpin domain 3 superfamily / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 3 / Rad4 beta-hairpin domain 1 ...DNA repair protein Rad4 / DNA repair protein Rad4, subgroup / Rad4/PNGase transglutaminase-like fold / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4, beta-hairpin domain 3 superfamily / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 3 / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4 transglutaminase-like domain / Transglutaminase-like superfamily / 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) / PH-domain like / Papain-like cysteine peptidase superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
DNA repair protein RAD4 / General transcription and DNA repair factor IIH subunit TFB1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsLafrance-Vanasse, J. / Arseneault, G. / Cappadocia, L. / Legault, P. / Omichinski, J.G.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structural and functional evidence that Rad4 competes with Rad2 for binding to the Tfb1 subunit of TFIIH in NER.
Authors: Lafrance-Vanasse, J. / Arseneault, G. / Cappadocia, L. / Legault, P. / Omichinski, J.G.
History
DepositionNov 16, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 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: RNA polymerase II transcription factor B subunit 1
B: DNA repair protein RAD4


Theoretical massNumber of molelcules
Total (without water)17,8482
Polymers17,8482
Non-polymers00
Water00
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: 13249.011 Da / Num. of mol.: 1 / Fragment: UNP residues 2-115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: TFB1, YDR311W, D9740.3 / Production host: Escherichia coli (E. coli) / References: UniProt: P32776
#2: Protein/peptide DNA repair protein RAD4


Mass: 4598.561 Da / Num. of mol.: 1 / Fragment: UNP residues 76-115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RAD4, YER162C / Production host: Escherichia coli (E. coli) / References: UniProt: P14736

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1262D 1H-15N HSQC
1352D 1H-13C HSQC
1443D CBCA(CO)NH
1543D HNCO
1643D HN(CA)CB
1743D H(CCO)NH
1853D (H)CCH-COSY
1963D 1H-15N NOESY
11053D 1H-13C NOESY
11122D 1H-13C HSQC
11213D CBCA(CO)NH
11313D HNCO
11413D HN(CA)CB
11513D H(CCO)NH
11623D (H)CCH-COSY
11733D 1H-15N NOESY
11823D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] Tfb1, 1.25 mM Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] Tfb1, 1.25 mM Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 100% D2O100% D2O
31 mM [U-100% 15N] Tfb1, 1.25 mM Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
41.25 mM Tfb1, 1 mM [U-100% 13C; U-100% 15N] Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
51.25 mM Tfb1, 1 mM [U-100% 13C; U-100% 15N] Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 100% D2O100% D2O
61.25 mM Tfb1, 1 mM [U-100% 15N] Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTfb1-1[U-100% 13C; U-100% 15N]1
1.25 mMRad4-21
20 mMsodium phosphate-31
1 mMEDTA-41
1 mMDTT-51
1 mMTfb1-6[U-100% 13C; U-100% 15N]2
1.25 mMRad4-72
20 mMsodium phosphate-82
1 mMEDTA-92
1 mMDTT-102
1 mMTfb1-11[U-100% 15N]3
1.25 mMRad4-123
20 mMsodium phosphate-133
1 mMEDTA-143
1 mMDTT-153
1.25 mMTfb1-164
1 mMRad4-17[U-100% 13C; U-100% 15N]4
20 mMsodium phosphate-184
1 mMEDTA-194
1 mMDTT-204
1.25 mMTfb1-215
1 mMRad4-22[U-100% 13C; U-100% 15N]5
20 mMsodium phosphate-235
1 mMEDTA-245
1 mMDTT-255
1.25 mMTfb1-266
1 mMRad4-27[U-100% 15N]6
20 mMsodium phosphate-286
1 mMEDTA-296
1 mMDTT-306
Sample conditionsIonic strength: 20 / 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 software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
VNMRVariancollection
VnmrJVariancollection
NMRViewJohnson, One Moon Scientificdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CcpNMR_2.1CCPNdata analysis
CcpNMR_2.1CCPNchemical shift assignment
CcpNMR_2.1CCPNpeak picking
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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