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- PDB-4wfq: Crystal structure of TFIIH subunit -

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Basic information

Entry
Database: PDB / ID: 4wfq
TitleCrystal structure of TFIIH subunit
ComponentsSuppressor of stem-loop protein 1
KeywordsTRANSCRIPTION / Helicase activator
Function / homology
Function and homology information


nucleotide-excision repair factor 3 complex / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape ...nucleotide-excision repair factor 3 complex / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / 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 / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / ubiquitin protein ligase activity / transcription by RNA polymerase II / regulation of transcription by RNA polymerase II / zinc ion binding
Similarity search - Function
TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / von Willebrand factor, type A domain / C1-like domain superfamily / von Willebrand factor (vWF) type A domain / VWFA domain profile. ...TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / von Willebrand factor, type A domain / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
General transcription and DNA repair factor IIH subunit SSL1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsCho, Y. / Kim, J.S. / Lim, H.S.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal structure of the Rad3/XPD regulatory domain of Ssl1/p44
Authors: Kim, J.S. / Saint-Andre, C. / Lim, H.S. / Hwang, C.S. / Egly, J.M. / Cho, Y.
History
DepositionSep 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Suppressor of stem-loop protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5983
Polymers21,4101
Non-polymers1882
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-4 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.594, 78.594, 83.903
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Suppressor of stem-loop protein 1 / General transcription and DNA repair factor IIH subunit SSL1 / TFIIH subunit SSL1


Mass: 21409.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SSL1, YLR005W / Production host: Escherichia coli (E. coli) / References: UniProt: Q04673
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 20596 / % possible obs: 100 % / Redundancy: 20.2 % / Net I/σ(I): 27.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementResolution: 2.4→28.68 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2136 608 5.04 %
Rwork0.1946 --
obs0.1955 12054 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1498 0 11 55 1564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081531
X-RAY DIFFRACTIONf_angle_d1.172071
X-RAY DIFFRACTIONf_dihedral_angle_d15.175584
X-RAY DIFFRACTIONf_chiral_restr0.083244
X-RAY DIFFRACTIONf_plane_restr0.005267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.64150.27591730.23392757X-RAY DIFFRACTION99
2.6415-3.02330.30171590.23732831X-RAY DIFFRACTION100
3.0233-3.80770.20811320.19652865X-RAY DIFFRACTION100
3.8077-28.68180.17581440.17322993X-RAY DIFFRACTION100

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