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- PDB-3dom: Crystal Structure of the complex between Tfb5 and the C-terminal ... -

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Basic information

Entry
Database: PDB / ID: 3dom
TitleCrystal Structure of the complex between Tfb5 and the C-terminal domain of Tfb2
Components
  • RNA polymerase II transcription factor B subunit 2
  • RNA polymerase II transcription factor B subunit 5
KeywordsTRANSCRIPTION / protein-protein complex / heterodimer / beta-alpha-beta split / beta-strand addition / DNA damage / DNA excision / DNA repair / Nucleus / Transcription regulation
Function / homology
Function and homology information


nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening ...nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / 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 / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / Gap-filling DNA repair synthesis and ligation in TC-NER / ATPase activator activity / Dual incision in TC-NER / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / double-stranded DNA binding / transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Alpha-Beta Plaits - #2610 / TFB5-like / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / TFIIH subunit TTDA/Tfb5 / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / Transcription factor TFIIH complex subunit Tfb5 ...Alpha-Beta Plaits - #2610 / TFB5-like / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / TFIIH subunit TTDA/Tfb5 / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / Transcription factor TFIIH complex subunit Tfb5 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
General transcription and DNA repair factor IIH subunit TFB2 / General transcription and DNA repair factor IIH subunit TFB5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsKainov, D.E. / Cavarelli, J. / Egly, J.M. / Poterszman, A.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural basis for group A trichothiodystrophy
Authors: Kainov, D.E. / Vitorino, M. / Cavarelli, J. / Poterszman, A. / Egly, J.M.
#1: Journal: J.Mol.Biol. / Year: 2007
Title: Solution structure and self-association properties of the p8 TFIIH subunit responsible for trichothiodystrophy
Authors: Vitorino, M. / Coin, F. / Zlobinskaya, O. / Atkinson, R.A. / Moras, D. / Egly, J.M. / Potesrzman, A. / Kieffer, B.
History
DepositionJul 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA polymerase II transcription factor B subunit 2
B: RNA polymerase II transcription factor B subunit 5
C: RNA polymerase II transcription factor B subunit 2
D: RNA polymerase II transcription factor B subunit 5


Theoretical massNumber of molelcules
Total (without water)41,5244
Polymers41,5244
Non-polymers00
Water1,74797
1
A: RNA polymerase II transcription factor B subunit 2
B: RNA polymerase II transcription factor B subunit 5


Theoretical massNumber of molelcules
Total (without water)20,7622
Polymers20,7622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-11.6 kcal/mol
Surface area7990 Å2
MethodPISA
2
C: RNA polymerase II transcription factor B subunit 2
D: RNA polymerase II transcription factor B subunit 5


Theoretical massNumber of molelcules
Total (without water)20,7622
Polymers20,7622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-8.5 kcal/mol
Surface area9030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.583, 103.593, 114.345
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RNA polymerase II transcription factor B subunit 2 / TFIIH subunit TFB2 / RNA polymerase II transcription factor B p52 subunit / RNA polymerase II ...TFIIH subunit TFB2 / RNA polymerase II transcription factor B p52 subunit / RNA polymerase II transcription factor B 52 kDa subunit / General transcription and DNA repair factor IIH subunit TFB2


Mass: 12649.552 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TFB2 / Plasmid: pSKB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q02939
#2: Protein RNA polymerase II transcription factor B subunit 5 / TFIIH subunit TFB5 / General transcription and DNA repair factor IIH subunit TFB5


Mass: 8112.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TFB5 / Plasmid: pSKB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q3E7C1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG3350 MME, NaCl, Hepes, pH 7.5, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97923 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 13927 / % possible obs: 96.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.058 / Χ2: 1.971 / Net I/σ(I): 23.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.693.50.13113242.222191.9
2.69-2.840.11813611.974199.1
2.8-2.9340.09514051.79198.7
2.93-3.0840.07914061.828199.2
3.08-3.284.10.06913961.897198.5
3.28-3.5340.06613972.41197.9
3.53-3.8840.0614012.162197.2
3.88-4.454.10.0513991.885196.7
4.45-5.64.10.04614111.801195.6
5.6-503.90.04114271.799189.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
REFMAC5.4.0067refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementResolution: 2.6→30.7 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.874 / Occupancy max: 1 / Occupancy min: 1 / SU B: 17.766 / SU ML: 0.193 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.423 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 703 5.1 %RANDOM
Rwork0.202 ---
obs0.205 13816 95.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 34.03 Å2 / Biso mean: 11.513 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2--0.26 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 0 97 2323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222260
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.9823043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9565269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.76425.189106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.74115448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3321512
X-RAY DIFFRACTIONr_chiral_restr0.1230.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211638
X-RAY DIFFRACTIONr_mcbond_it0.6831.51360
X-RAY DIFFRACTIONr_mcangle_it1.35222200
X-RAY DIFFRACTIONr_scbond_it2.2773900
X-RAY DIFFRACTIONr_scangle_it3.7694.5843
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 49 -
Rwork0.235 842 -
all-891 -
obs--85.18 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.39753.0109-2.60634.2431-2.02393.8740.06780.1956-0.1882-0.10160.04760.04110.1648-0.2221-0.1154-0.22710.0133-0.0302-0.2344-0.0312-0.190610.067619.91490.3614
24.14171.4825-3.71585.4794-1.073610.3254-0.25390.1313-0.8816-0.04360.09770.11191.1349-0.28850.1562-0.0536-0.0049-0.0435-0.07610.02530.00494.32476.71485.9384
33.1202-2.18462.40512.7787-2.71084.5549-0.0407-0.21510.1147-0.14990.0336-0.04550.0198-0.36190.0071-0.16-0.00250.0198-0.226-0.0276-0.1255-0.9467-19.7323-3.8279
42.5347-2.35874.52633.897-3.879810.8824-0.34080.33720.6319-0.155-0.214-0.0661-0.99980.10210.55480.0214-0.0129-0.04430.01260.01180.0824-6.3543-7.4125-12.0027
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA437 - 50932 - 104
2X-RAY DIFFRACTION2BB2 - 591 - 58
3X-RAY DIFFRACTION3CC432 - 50727 - 102
4X-RAY DIFFRACTION4DD2 - 661 - 65

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