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- PDB-5xv8: Solution structure of the complex between UVSSA acidic region and... -

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Basic information

Entry
Database: PDB / ID: 5xv8
TitleSolution structure of the complex between UVSSA acidic region and TFIIH p62 PH domain
Components
  • General transcription factor IIH subunit 1
  • UV-stimulated scaffold protein A
KeywordsNUCLEAR PROTEIN / DNA repair factor / general transcription factor / nucleotide excision repair / transcription-coupled repair
Function / homology
Function and homology information


RNA polymerase inhibitor activity / chromatin-protein adaptor activity / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / nuclear thyroid hormone receptor binding / 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 ...RNA polymerase inhibitor activity / chromatin-protein adaptor activity / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / nuclear thyroid hormone receptor binding / 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 / RNA polymerase II complex binding / RNA Polymerase I Transcription Initiation / site of DNA damage / 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 / transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / response to UV / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / hormone-mediated signaling pathway / RNA Polymerase II Pre-transcription Events / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / 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 / chromosome / transcription by RNA polymerase II / protein ubiquitination / DNA repair / chromatin binding / positive regulation of DNA-templated transcription / nucleoplasm / nucleus
Similarity search - Function
UV-stimulated scaffold protein A / : / : / Uncharacterized conserved protein (DUF2043) / UVSSA N-terminal domain / Zinc finger UVSSA-type profile. / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain ...UV-stimulated scaffold protein A / : / : / Uncharacterized conserved protein (DUF2043) / UVSSA N-terminal domain / Zinc finger UVSSA-type profile. / 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 / ENTH/VHS / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
General transcription factor IIH subunit 1 / UV-stimulated scaffold protein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsOkuda, M. / Nishimura, Y.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Common TFIIH recruitment mechanism in global genome and transcription-coupled repair subpathways
Authors: Okuda, M. / Nakazawa, Y. / Guo, C. / Ogi, T. / Nishimura, Y.
History
DepositionJun 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: UV-stimulated scaffold protein A
B: General transcription factor IIH subunit 1


Theoretical massNumber of molelcules
Total (without water)17,9582
Polymers17,9582
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2250 Å2
ΔGint3 kcal/mol
Surface area9200 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 UV-stimulated scaffold protein A


Mass: 5507.810 Da / Num. of mol.: 1 / Fragment: UNP residues 390-434
Source method: isolated from a genetically manipulated source
Details: The three amino acids (GSM) at the N terminus do not derive from UVSSA.
Source: (gene. exp.) Homo sapiens (human) / Gene: UVSSA, KIAA1530 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YD98
#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 2-108
Source method: isolated from a genetically manipulated source
Details: The two amino acids (GS) at the N terminus do not derive from TFIIH p62.
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
121isotropic23D CBCA(CO)NH
131isotropic23D HNCO
141isotropic23D HBHA(CO)NH
151isotropic23D C(CO)NH
161isotropic23D H(CCO)NH
1231isotropic23D HNHB
171isotropic13D 1H-15N NOESY
182isotropic12D 1H-13C HSQC
192isotropic12D 1H-13C HSQC aromatic
1102isotropic13D 1H-13C NOESY
1113isotropic12D 1H-15N HSQC
1203isotropic23D CBCA(CO)NH
1193isotropic23D HNCO
1183isotropic23D HBHA(CO)NH
1173isotropic23D C(CO)NH
1163isotropic23D H(CCO)NH
1213isotropic23D (H)CCH-TOCSY
1223isotropic23D HNHB
1153isotropic13D 1H-15N NOESY
1144isotropic12D 1H-13C HSQC
1134isotropic12D 1H-13C HSQC aromatic
1124isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.40 mM [U-99% 13C; U-99% 15N] UVSSA, 0.48 mM TFIIH p62, 90% H2O/10% D2OUVSSA-p62_H2O90% H2O/10% D2O
solution20.40 mM [U-99% 13C; U-99% 15N] UVSSA, 0.48 mM TFIIH p62, 100% D2OUVSSA-p62_D2O100% D2O
solution30.40 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.48 mM UVSSA, 90% H2O/10% D2Op62-UVSSA_H2O90% H2O/10% D2O
solution40.40 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.48 mM UVSSA, 100% D2Op62-UVSSA_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.40 mMUVSSA[U-99% 13C; U-99% 15N]1
0.48 mMTFIIH p62natural abundance1
0.40 mMUVSSA[U-99% 13C; U-99% 15N]2
0.48 mMTFIIH p62natural abundance2
0.40 mMTFIIH p62[U-99% 13C; U-99% 15N]3
0.48 mMUVSSAnatural abundance3
0.40 mMTFIIH p62[U-99% 13C; U-99% 15N]4
0.48 mMUVSSAnatural abundance4
Sample conditionsDetails: 20 mM KPB (pH6.8), 5mM d-DTT / Ionic strength: 20 mM / Label: 1 / pH: 6.8 / Pressure: 760 mmHg / 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
ProcheckNMRLaskowski and MacArthurdata analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 6
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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