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- PDB-5gow: Solution structure of the complex between DP1 acidic region and T... -

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Basic information

Entry
Database: PDB / ID: 5gow
TitleSolution structure of the complex between DP1 acidic region and TFIIH p62 PH domain
Components
  • DP1
  • General transcription factor IIH subunit 1
KeywordsTRANSCRIPTION / Transcription factor / General transcription factor / Cell cycle / Transcription activation / Solution structure
Function / homology
Function and homology information


regulation of DNA biosynthetic process / negative regulation of fat cell proliferation / Rb-E2F complex / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / Transcription of E2F targets under negative control by DREAM complex / Activation of NOXA and translocation to mitochondria ...regulation of DNA biosynthetic process / negative regulation of fat cell proliferation / Rb-E2F complex / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / Transcription of E2F targets under negative control by DREAM complex / Activation of NOXA and translocation to mitochondria / anoikis / nuclear thyroid hormone receptor binding / Activation of PUMA and translocation to mitochondria / RNA Polymerase I Transcription Termination / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / mRNA Capping / G1/S-Specific Transcription / Transcriptional Regulation by E2F6 / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / RNA Polymerase I Transcription Initiation / G0 and Early G1 / epidermis development / positive regulation of G1/S transition of mitotic cell cycle / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / Cyclin E associated events during G1/S transition / transcription by RNA polymerase I / Cyclin A:Cdk2-associated events at S phase entry / cis-regulatory region sequence-specific DNA binding / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / positive regulation of DNA-binding transcription factor activity / hormone-mediated signaling pathway / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / Oncogene Induced Senescence / RNA Polymerase I Promoter Escape / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / NoRC negatively regulates rRNA expression / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Pre-NOTCH Transcription and Translation / Cyclin D associated events in G1 / RNA polymerase II transcription regulator complex / Transcriptional regulation of granulopoiesis / Oxidative Stress Induced Senescence / DNA-binding transcription factor binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / protein domain specific binding / DNA repair / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Transcription factor DP, C-terminal / Transcription factor DP / Transcription factor DP, C-terminal domain superfamily / Transcription factor DP / Transcription factor DP / E2F-DP heterodimerization region / E2F/DP family, winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / TFIIH p62 subunit, N-terminal ...Transcription factor DP, C-terminal / Transcription factor DP / Transcription factor DP, C-terminal domain superfamily / Transcription factor DP / Transcription factor DP / E2F-DP heterodimerization region / E2F/DP family, winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
General transcription factor IIH subunit 1 / Transcription factor Dp-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsOkuda, M. / Nishimura, Y.
CitationJournal: J. Mol. Biol. / Year: 2016
Title: The Interaction Mode of the Acidic Region of the Cell Cycle Transcription Factor DP1 with TFIIH
Authors: Okuda, M. / Araki, K. / Ohtani, K. / Nishimura, Y.
History
DepositionJul 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DP1
B: General transcription factor IIH subunit 1


Theoretical massNumber of molelcules
Total (without water)14,7292
Polymers14,7292
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1980 Å2
ΔGint5 kcal/mol
Surface area6460 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide DP1


Mass: 2279.022 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14186*PLUS
#2: Protein General transcription factor IIH subunit 1 / Basic transcription factor 2 62 kDa subunit / BTF2 p62 / General transcription factor IIH ...Basic transcription factor 2 62 kDa subunit / BTF2 p62 / General transcription factor IIH polypeptide 1 / TFIIH basal transcription factor complex p62 subunit


Mass: 12450.445 Da / Num. of mol.: 1 / Fragment: UNP residues 1-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H1, BTF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P32780

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
132isotropic12D 1H-13C HSQC aromatic
141isotropic23D CBCA(CO)NH
151isotropic23D HNCO
161isotropic23D HBHA(CO)NH
171isotropic23D C(CO)NH
181isotropic23D H(CCO)NH
191isotropic13D 1H-15N NOESY
1102isotropic13D 1H-13C NOESY
1113isotropic12D 1H-15N HSQC
1124isotropic12D 1H-13C HSQC
1134isotropic12D 1H-13C HSQC aromatic
1143isotropic23D CBCA(CO)NH
1153isotropic23D HNCO
1163isotropic23D HBHA(CO)NH
1173isotropic23D C(CO)NH
1183isotropic23D H(CCO)NH
1193isotropic13D 1H-15N NOESY
1204isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.35 mM [U-99% 13C; U-99% 15N] DP1, 0.42 mM TFIIH p62, 90% H2O/10% D2ODP1-p6290% H2O/10% D2O
solution20.35 mM [U-99% 13C; U-99% 15N] DP1, 0.42 mM TFIIH p62, 100% D2ODP1-p62100% D2O
solution30.35 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.42 mM DP1, 90% H2O/10% D2Op62-DP190% H2O/10% D2O
solution40.35 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.42 mM DP1, 100% D2Op62-DP1100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.35 mMDP1[U-99% 13C; U-99% 15N]1
0.42 mMTFIIH p62natural abundance1
0.35 mMDP1[U-99% 13C; U-99% 15N]2
0.42 mMTFIIH p62natural abundance2
0.35 mMTFIIH p62[U-99% 13C; U-99% 15N]3
0.42 mMDP1natural abundance3
0.35 mMTFIIH p62[U-99% 13C; U-99% 15N]4
0.42 mMDP1natural abundance4
Sample conditionsIonic strength: 0.02 M / Label: condition_1 / pH: 6.8 / Pressure: 760 Torr / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III9501
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 4
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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