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- PDB-2gs0: NMR structure of the complex between the PH domain of the Tfb1 su... -

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Basic information

Entry
Database: PDB / ID: 2gs0
TitleNMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the activation domain of p53
Components
  • Cellular tumor antigen p53
  • RNA polymerase II transcription factor B subunit 1
KeywordsTRANSCRIPTION / p53 / TFIIH / Tfb1 / activation / PH domain
Function / homology
Function and homology information


phosphatidylinositol-5-phosphate binding / nucleotide-excision repair factor 3 complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition ...phosphatidylinositol-5-phosphate binding / nucleotide-excision repair factor 3 complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / Activation of NOXA and translocation to mitochondria / regulation of cell cycle G2/M phase transition / oligodendrocyte apoptotic process / negative regulation of miRNA processing / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / mRNA transcription / bone marrow development / positive regulation of programmed necrotic cell death / circadian behavior / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / glucose catabolic process to lactate via pyruvate / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase regulator activity / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuroblast proliferation / RNA Pol II CTD phosphorylation and interaction with CE / mitochondrial DNA repair / Formation of the Early Elongation Complex / T cell lineage commitment / mRNA Capping / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / 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 / ER overload response / RNA Polymerase II Pre-transcription Events / thymocyte apoptotic process / B cell lineage commitment / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / negative regulation of mitophagy / Formation of TC-NER Pre-Incision Complex / negative regulation of DNA replication / entrainment of circadian clock by photoperiod / RNA Polymerase I Promoter Escape / negative regulation of telomere maintenance via telomerase / Zygotic genome activation (ZGA) / positive regulation of release of cytochrome c from mitochondria / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / necroptotic process / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / Gap-filling DNA repair synthesis and ligation in TC-NER / TFIID-class transcription factor complex binding / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / intrinsic apoptotic signaling pathway by p53 class mediator / rRNA transcription / negative regulation of reactive oxygen species metabolic process / Transcriptional Regulation by VENTX / cellular response to UV-C / replicative senescence / general transcription initiation factor binding / Dual incision in TC-NER / cellular response to actinomycin D / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of RNA polymerase II transcription preinitiation complex assembly / neuroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of execution phase of apoptosis / viral process / Pyroptosis / hematopoietic stem cell differentiation / response to X-ray / embryonic organ development / chromosome organization / type II interferon-mediated signaling pathway / somitogenesis / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / hematopoietic progenitor cell differentiation / glial cell proliferation
Similarity search - Function
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 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 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 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / p53-like transcription factor, DNA-binding / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Cellular tumor antigen p53 / General transcription and DNA repair factor IIH subunit TFB1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodSOLUTION NMR / Simulated annealing, with a combination of torsion angle, Cartesian dynamics.
AuthorsDi Lello, P. / Jones, T.N. / Nguyen, B.D. / Legault, P. / Omichinski, J.G.
CitationJournal: Mol.Cell / Year: 2006
Title: Structure of the Tfb1/p53 complex: Insights into the interaction between the p62/Tfb1 subunit of TFIIH and the activation domain of p53.
Authors: Di Lello, P. / Jenkins, L.M. / Jones, T.N. / Nguyen, B.D. / Hara, T. / Yamaguchi, H. / Dikeakos, J.D. / Appella, E. / Legault, P. / Omichinski, J.G.
History
DepositionApr 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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 1.4May 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: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)18,9222
Polymers18,9222
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 67structures with the lowest energy
RepresentativeModel #1lowest 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 kDa subunit


Mass: 12903.701 Da / Num. of mol.: 1 / Mutation: M1P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TFB1 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 / References: UniProt: P32776
#2: Protein Cellular tumor antigen p53 / Tumor suppressor p53


Mass: 6018.665 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53 / Plasmid: pGEX-2TK / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 / References: UniProt: P04637

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-edited NOESY-HSQC
1223D 13C-edited HMQC-NOESY
1323D 15N-13C {F1}-filtered {F3}-edited NOESY
1412D 1H-15N HSQC
1533D 15N-edited NOESY-HSQC
1643D 13C-edited HMQC-NOESY
1743D 15N-13C {F1}-filtered {F3}-edited NOESY
1832D 1H-15N HSQC
1922D CT-HMQC
11042D CT-HMQ
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM Tfb1 U-15N, 1.0 mM p53 unlabeled, 1.00 mM EDTA, 20 mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
21.0 mM Tfb1 U-15N,13C, 1.0 mM p53 unlabeled, 1.00 mM EDTA, 20 mM phosphate buffer; 100% D20100% D20
31.0 mM p53 U-15N, 1.0 mM Tfb1 unlabeled, 1.00 mM EDTA, 20 mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
41.0 mM p53 U-15N, 1.0 mM Tfb1 unlabeled, 1.00 mM EDTA, 20 mM phosphate buffer; 100% D20100% D20
Sample conditionsIonic strength: 20 mM sodium phosphate / pH: 6.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY5001
Varian UNITYVarianUNITY6002
Varian UNITYVarianUNITY8003

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1.CVariancollection
NMRPipe2.2F. Delaglio, S. Grzesiek, G.W. Vuister, G. Zhu, J. Pfeifer and A. Baxprocessing
NMRView5.0.4B.A. Johnson and R.A. Blevinsdata analysis
CNS1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenstructure solution
CNS1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenrefinement
RefinementMethod: Simulated annealing, with a combination of torsion angle, Cartesian dynamics.
Software ordinal: 1
Details: The three-dimensional structures of the complex Tfb1/p53 were determined using a set of 1720 NOE-derived distance restraints, 138 backbone dihedral angle (phi and psi) restraints and 26 ...Details: The three-dimensional structures of the complex Tfb1/p53 were determined using a set of 1720 NOE-derived distance restraints, 138 backbone dihedral angle (phi and psi) restraints and 26 distance restraints from hydrogen bonds. Because of the absence of medium-range, long-range and intermolecular NOEs involving residues 20-44 and 59-73 of p53 (chain B), these amino acids were not included in the calculations.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 67 / Conformers submitted total number: 20

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