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

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Basic information

Entry
Database: PDB / ID: 3dgp
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 / BETA-ALPHA-BETA SPILT / HETERODIMER / 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 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 ...nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / 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 / ATPase activator activity / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / 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 / SAD / Resolution: 1.8 Å
AuthorsKainov, D.E. / Cavarelli, J. / Egly, J.M. / Poterszman, A.
CitationJournal: 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.
History
DepositionJun 14, 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 1.2Feb 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


Theoretical massNumber of molelcules
Total (without water)17,5872
Polymers17,5872
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-6.6 kcal/mol
Surface area7730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.992, 99.992, 37.262
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein RNA polymerase II transcription factor B subunit 2 / RNA polymerase II transcription factor B p52 subunit / RNA polymerase II transcription factor B 52 ...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 / TFIIH subunit TFB2


Mass: 9474.843 Da / Num. of mol.: 1 / 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(DE3) / References: UniProt: Q02939
#2: Protein RNA polymerase II transcription factor B subunit 5 / General transcription and DNA repair factor IIH subunit TFB5 / TFIIH subunit TFB5


Mass: 8112.293 Da / Num. of mol.: 1
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(DE3) / References: UniProt: Q3E7C1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3.06 Å3/Da / Density % sol: 59.77 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 8.9
Details: Tris 20 mM, NaCl 50 mM, pH 8.9, EVAPORATION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9198 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 20032 / Num. obs: 19737 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 26
Reflection shellResolution: 1.8→1.87 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 7.3 / Num. unique all: 2181 / Rsym value: 0.249 / % possible all: 0.937

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.905 / SU B: 4.311 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23708 1006 5.1 %RANDOM
Rwork0.19707 ---
obs0.19905 18822 99.1 %-
all-20032 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.407 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20.56 Å20 Å2
2--1.12 Å20 Å2
3----1.68 Å2
Refine analyze
FreeObs
Luzzati sigma a0.107 Å0.103 Å
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1017 0 0 126 1143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221031
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.271.9821383
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0535123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30225.30649
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80315208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.909155
X-RAY DIFFRACTIONr_chiral_restr0.0970.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02746
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.2477
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2717
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9751.5637
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6621000
X-RAY DIFFRACTIONr_scbond_it2.4543439
X-RAY DIFFRACTIONr_scangle_it3.954.5383
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 84 -
Rwork0.212 1275 -
obs--91.76 %
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)
11.5438-0.31460.87610.9405-0.69523.8330.0209-0.0953-0.0998-0.02420.06990.0770.1044-0.2917-0.0908-0.0980.03160.00940.03840.0109-0.080719.50441.796525.9854
21.6168-0.91620.93523.8839-1.97543.3693-0.0647-0.14540.17610.130.08150.0695-0.2532-0.1066-0.0168-0.09150.0488-0.0029-0.002-0.0198-0.060111.753359.485616.1255
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA450 - 50817 - 75
2X-RAY DIFFRACTION2BB2 - 631 - 62

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