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- PDB-5o85: p34-p44 complex -

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Basic information

Entry
Database: PDB / ID: 5o85
Titlep34-p44 complex
Components
  • General transcription factor IIH subunit 2
  • General transcription factor IIH subunit 3
KeywordsTRANSCRIPTION / DNA repair / TFIIH / TFIIH interaction network / p34-p44 complex
Function / homology
Function and homology information


core TFIIH complex portion of holo TFIIH complex / G protein-coupled receptor internalization / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / RNA Polymerase I Transcription Termination / transcription preinitiation complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE ...core TFIIH complex portion of holo TFIIH complex / G protein-coupled receptor internalization / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / RNA Polymerase I Transcription Termination / transcription preinitiation complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / 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 / mRNA Capping / 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 / RNA Polymerase I Transcription Initiation / 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 / response to UV / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / 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 / NoRC negatively regulates rRNA expression / 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 / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase II / nuclear speck / DNA repair / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 ...TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / C1-like domain superfamily / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Zinc finger C2H2-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
General transcription factor IIH subunit 2 / General transcription factor IIH subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsRadu, L. / Poterszman, A.
Funding support France, 5items
OrganizationGrant numberCountry
French National Research AgencyANR-12-BSV8-0015-01 France
INCAINCA_9378 France
Association pour la Recherche sur le CancerSL120120304592 France
La ligue contre le cancerCCIR-GE 2013 and Post-doctoral fellowship to L.R. France
French National Research AgencyANR-10-INSB-05-01 France
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: The intricate network between the p34 and p44 subunits is central to the activity of the transcription/DNA repair factor TFIIH.
Authors: Radu, L. / Schoenwetter, E. / Braun, C. / Marcoux, J. / Koelmel, W. / Schmitt, D.R. / Kuper, J. / Cianferani, S. / Egly, J.M. / Poterszman, A. / Kisker, C.
History
DepositionJun 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.3Jan 17, 2024Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: General transcription factor IIH subunit 3
B: General transcription factor IIH subunit 2
C: General transcription factor IIH subunit 3
D: General transcription factor IIH subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,0268
Polymers157,7644
Non-polymers2624
Water00
1
A: General transcription factor IIH subunit 3
B: General transcription factor IIH subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0134
Polymers78,8822
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: General transcription factor IIH subunit 3
D: General transcription factor IIH subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0134
Polymers78,8822
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.407, 120.388, 128.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein General transcription factor IIH subunit 3 / Basic transcription factor 2 34 kDa subunit / BTF2 p34 / General transcription factor IIH ...Basic transcription factor 2 34 kDa subunit / BTF2 p34 / General transcription factor IIH polypeptide 3 / TFIIH basal transcription factor complex p34 subunit


Mass: 34416.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13889
#2: Protein General transcription factor IIH subunit 2 / Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH ...Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH polypeptide 2 / TFIIH basal transcription factor complex p44 subunit


Mass: 44465.934 Da / Num. of mol.: 2 / Mutation: C381S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H2, BTF2P44 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13888
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 mM Tris-HCl or Hepes (pH 7.0 to 8.5) and 20-40% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.28236 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28236 Å / Relative weight: 1
ReflectionResolution: 3.19→46.55 Å / Num. obs: 141682 / % possible obs: 99.4 % / Redundancy: 13.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.061 / Net I/σ(I): 8.9
Reflection shellResolution: 3.19→3.39 Å / Redundancy: 12.8 % / Rmerge(I) obs: 3.092 / Mean I/σ(I) obs: 1 / Num. unique all: 19316 / CC1/2: 0.593 / Rpim(I) all: 1.272 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4pn7

4pn7


Resolution: 3.4→40.7 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 38.54
RfactorNum. reflection% reflectionSelection details
Rfree0.29 445 4.94 %Random selection
Rwork0.24 ---
obs0.233 9015 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.4→40.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3845 0 4 0 3849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033912
X-RAY DIFFRACTIONf_angle_d0.6265283
X-RAY DIFFRACTIONf_dihedral_angle_d15.4072364
X-RAY DIFFRACTIONf_chiral_restr0.043620
X-RAY DIFFRACTIONf_plane_restr0.004663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4002-3.8920.39361510.33452807X-RAY DIFFRACTION100
3.892-4.90250.28781470.22852816X-RAY DIFFRACTION100
4.9025-43.95880.26391470.20832947X-RAY DIFFRACTION100

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