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

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Basic information

Entry
Database: PDB / ID: 2lox
TitleNMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad2
Components
  • DNA repair protein RAD2
  • RNA polymerase II transcription factor B subunit 1
KeywordsTRANSCRIPTION/HYDROLASE / TRANSCRIPTION-HYDROLASE complex
Function / homology
Function and homology information


phosphatidylinositol-5-phosphate binding / single-stranded DNA endodeoxyribonuclease activity / 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 / TP53 Regulates Transcription of DNA Repair Genes ...phosphatidylinositol-5-phosphate binding / single-stranded DNA endodeoxyribonuclease activity / 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 / 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 / Dual incision in TC-NER / DNA endonuclease activity / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / single-stranded DNA binding / transcription by RNA polymerase II / Hydrolases; Acting on ester bonds / DNA repair / nucleus / metal ion binding / cytosol
Similarity search - Function
XPG/Rad2 endonuclease, eukaryotes / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region ...XPG/Rad2 endonuclease, eukaryotes / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / 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 / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
DNA repair protein RAD2 / 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. / Legault, P. / Omichinski, J.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural and functional characterization of interactions involving the Tfb1 subunit of TFIIH and the NER factor Rad2.
Authors: Lafrance-Vanasse, J. / Arseneault, G. / Cappadocia, L. / Chen, H.T. / Legault, P. / Omichinski, J.G.
History
DepositionJan 27, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Jul 11, 2012Group: Database references
Revision 1.3Jun 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 1.4May 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 RAD2


Theoretical massNumber of molelcules
Total (without water)19,2632
Polymers19,2632
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: D9740.3, TFB1, YDR311W / Production host: Escherichia coli (E. coli) / Strain (production host): Topp2 / References: UniProt: P32776
#2: Protein DNA repair protein RAD2


Mass: 6014.244 Da / Num. of mol.: 1 / Fragment: UNP residues 642-690
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RAD2, YGR258C / Production host: Escherichia coli (E. coli) / Strain (production host): Topp2
References: UniProt: P07276, Hydrolases; Acting on ester bonds

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1222D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D H(CCO)NH
1723D (H)CCH-COSY
1833D 1H-15N NOESY
1923D 1H-13C NOESY
11062D 1H-15N HSQC
11152D 1H-13C HSQC
11243D CBCA(CO)NH
11343D HNCO
11443D HN(CA)CB
11543D H(CCO)NH
11653D (H)CCH-COSY
11763D 1H-15N NOESY
11853D 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 Rad2, 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 Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 100% D2O100% D2O
31 mM [U-100% 15N] Tfb1, 1.25 mM Rad2, 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] Rad2, 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] Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 100% D2O100% D2O
61.25 mM Tfb1, 1 mM [U-100% 15N] Rad2, 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 mMRad2-21
20 mMsodium phosphate-31
1 mMEDTA-41
1 mMDTT-51
1 mMTfb1-6[U-100% 13C; U-100% 15N]2
1.25 mMRad2-72
20 mMsodium phosphate-82
1 mMEDTA-92
1 mMDTT-102
1 mMTfb1-11[U-100% 15N]3
1.25 mMRad2-123
20 mMsodium phosphate-133
1 mMEDTA-143
1 mMDTT-153
1.25 mMTfb1-164
1 mMRad2-17[U-100% 13C; U-100% 15N]4
20 mMsodium phosphate-184
1 mMEDTA-194
1 mMDTT-204
1.25 mMTfb1-215
1 mMRad2-22[U-100% 13C; U-100% 15N]5
20 mMsodium phosphate-235
1 mMEDTA-245
1 mMDTT-255
1.25 mMTfb1-266
1 mMRad2-27[U-100% 15N]6
20 mMsodium phosphate-286
1 mMEDTA-296
1 mMDTT-306
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
CcpNMR2.1CCPNchemical shift assignment
CcpNMR2.1CCPNdata analysis
CcpNMR2.1CCPNpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRViewJohnson, One Moon Scientificdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
VNMRVariancollection
TALOSCornilescu, Delaglio and Baxdata analysis
VnmrJVariancollection
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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