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- PDB-2k2u: NMR Structure of the complex between Tfb1 subunit of TFIIH and th... -

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Basic information

Entry
Database: PDB / ID: 2k2u
TitleNMR Structure of the complex between Tfb1 subunit of TFIIH and the activation domain of VP16
Components
  • Alpha trans-inducing protein
  • RNA polymerase II transcription factor B subunit 1
KeywordsTRANSCRIPTION / VP16 / TFIIH / Tfb1 / Activation / PH Domain / Protein Structure Complex / DNA damage / DNA repair / Nucleus / Transcription regulation / DNA-binding
Function / homology
Function and homology information


DNA-templated viral transcription / viral tegument / 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 ...DNA-templated viral transcription / viral tegument / 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 / Dual incision in TC-NER / transcription by RNA polymerase I / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / transcription by RNA polymerase II / DNA repair / host cell nucleus / regulation of DNA-templated transcription / DNA binding / nucleus / cytosol
Similarity search - Function
Alpha trans-inducing protein (Alpha-TIF) / Herpes simplex virus, Tegument protein VP16, C-terminal / Alpha trans-inducing (Alpha-TIF) superfamily / Alpha trans-inducing protein (Alpha-TIF) / Herpes simplex virus virion protein 16 C terminal / Alpha trans-inducing protein (Alpha-TIF) / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain ...Alpha trans-inducing protein (Alpha-TIF) / Herpes simplex virus, Tegument protein VP16, C-terminal / Alpha trans-inducing (Alpha-TIF) superfamily / Alpha trans-inducing protein (Alpha-TIF) / Herpes simplex virus virion protein 16 C terminal / Alpha trans-inducing protein (Alpha-TIF) / 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 / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Tegument protein VP16 / General transcription and DNA repair factor IIH subunit TFB1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Human herpesvirus 1 (Herpes simplex virus type 1)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, simulated annealing
AuthorsLanglois, C. / Mas, C. / Di Lello, P. / Miller Jenkins, P.M. / Legault, J. / Omichinski, J.G.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: NMR Structure of the Complex between the Tfb1 Subunit of TFIIH and the Activation Domain of VP16: Structural Similarities between VP16 and p53.
Authors: Langlois, C. / Mas, C. / Di Lello, P. / Jenkins, L.M. / Legault, P. / Omichinski, J.G.
History
DepositionApr 11, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: 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: RNA polymerase II transcription factor B subunit 1
B: Alpha trans-inducing protein


Theoretical massNumber of molelcules
Total (without water)16,7212
Polymers16,7212
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #5lowest energy

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Components

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


Mass: 12903.701 Da / Num. of mol.: 1 / Fragment: PH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Species: Cerevisiae / Gene: TFB1, YDR311W, D9740.3 / Plasmid: plasmid / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 / References: UniProt: P32776
#2: Protein/peptide Alpha trans-inducing protein / Vmw65 / ICP25 / VP16 protein / Alpha-TIF


Mass: 3817.064 Da / Num. of mol.: 1 / Fragment: Transcription activation domain 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Strain: strain F / Gene: UL48 / Plasmid: plasmid / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 / References: UniProt: P04486

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
122HNCO
132HN(CA)CB
142(HB)CBCA(CO)NNH
152C(CO)NNH
1613D-15N-EDITED-NOESY-HSQC
1723D-13C-EDITED-HMQC-NOESY
1823D-15N-13C-FILTRED-EDITED-NOESY
1922D 1H-13C HSQC
11032D 1H-15N HSQC
11143D HNCO
11243D HN(CA)CB
1134(HB)CBCA(CO)NNH
1144C(CO)NNH
11533D-15N-EDITED-NOESY-HSQC
11643D-15N-13C-EDITED-NOESY-HSQC
11743D-15N-13C-FILTRED-EDITED-NOESY
11842D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-99% 15N] Tfb1, 1.0 mM VP16, 90% H2O, 10% D2O90% H2O/10% D2O
21.0 mM [U-99% 13C; U-99% 15N] Tfb1, 1.0 mM VP16, 100% D2O100% D2O
31.0 mM [U-99% 15N] VP16, 1.0 mM Tfb1, 90% H2O, 10% D2O90% H2O/10% D2O
41.0 mM [U-99% 13C; U-99% 15N] VP16, 1.0 mM Tfb1, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMTfb1[U-99% 15N]1
1.0 mMVP161
1.0 mMTfb1[U-99% 13C; U-99% 15N]2
1.0 mMVP162
1.0 mMVP16[U-99% 15N]3
1.0 mMTfb13
1.0 mMVP16[U-99% 13C; U-99% 15N]4
1.0 mMTfb14
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

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing, torsion angle dynamics, simulated annealing
Software ordinal: 1
Details: The three-dimensional structures of the complex Tfb1/VP16 were determined using a set of 1568 NOE-derived distance restraints, 158 backbone dihedral angle (Phi and Psi)restraints and 36 ...Details: The three-dimensional structures of the complex Tfb1/VP16 were determined using a set of 1568 NOE-derived distance restraints, 158 backbone dihedral angle (Phi and Psi)restraints and 36 distance restraints from hydrogen bounds., The three-dimensional structures of the complex Tfb1/VP16 were determined using a set of 1568 NOE-derived distance restraints, 158 backbone dihedral angle (Phi and Psi)restraints and 36 distance restraints fron hydrogen bounds.
NMR constraintsNOE constraints total: 1568 / NOE intraresidue total count: 578 / NOE long range total count: 309 / NOE medium range total count: 194 / NOE sequential total count: 446 / Protein phi angle constraints total count: 79 / Protein psi angle constraints total count: 79
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20
NMR ensemble rmsBond angle rms dev: 0.395 ° / Covalent bond rms dev: 0.0025 Å / Dihedral angles rms dev: 29.899 ° / Improper torsion angle rms dev: 0.281 °

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