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- PDB-6trs: Crystal structure of TFIIH subunit p52 in complex with p8 -

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Basic information

Entry
Database: PDB / ID: 6trs
TitleCrystal structure of TFIIH subunit p52 in complex with p8
Components
  • RNA polymerase II transcription factor B subunit 2
  • Uncharacterized protein
KeywordsTRANSCRIPTION / TFIIH / DNA repair
Function / homology
Function and homology information


transcription factor TFIIH holo complex / transcription factor TFIIH core complex / ATPase activator activity / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter
Similarity search - Function
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
Similarity search - Domain/homology
RNA polymerase II transcription factor B subunit 2 / General transcription and DNA repair factor IIH subunit TFB5
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsKoelmel, W. / Kuper, J. / Schoenwetter, E. / Kisker, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KI-562/11-1 Germany
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: How to limit the speed of a motor: the intricate regulation of the XPB ATPase and translocase in TFIIH.
Authors: Kappenberger, J. / Koelmel, W. / Schoenwetter, E. / Scheuer, T. / Woerner, J. / Kuper, J. / Kisker, C.
History
DepositionDec 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 23, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 2
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)104,0543
Polymers104,0543
Non-polymers00
Water00
1
A: RNA polymerase II transcription factor B subunit 2


Theoretical massNumber of molelcules
Total (without water)46,2451
Polymers46,2451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16100 Å2
2
B: RNA polymerase II transcription factor B subunit 2
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)57,8092
Polymers57,8092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-10 kcal/mol
Surface area24750 Å2
Unit cell
Length a, b, c (Å)74.216, 85.954, 92.172
Angle α, β, γ (deg.)90.000, 94.930, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RNA polymerase II transcription factor B subunit 2


Mass: 46245.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0044720 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S965
#2: Protein Uncharacterized protein


Mass: 11563.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0052580 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SDQ1

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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: 2.91 Å3/Da / Density % sol: 57.79 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 8.5 / Details: ammonium chloride, PEG 4000, TRIS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.68→19.92 Å / Num. obs: 17307 / % possible obs: 88.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 53.57 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.28 / Rpim(I) all: 0.14 / Net I/σ(I): 5.7
Reflection shellResolution: 2.68→2.95 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.429 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 865 / CC1/2: 0.318 / Rpim(I) all: 0.715 / % possible all: 49.5

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Processing

Software
NameVersionClassification
XDSdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
Aimlessdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→19.92 Å / Cor.coef. Fo:Fc: 0.849 / Cor.coef. Fo:Fc free: 0.818 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.434
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1091 6.38 %RANDOM
Rwork0.216 ---
obs0.217 17099 52.7 %-
Displacement parametersBiso max: 145.28 Å2 / Biso mean: 53.17 Å2 / Biso min: 19.73 Å2
Baniso -1Baniso -2Baniso -3
1-15.11 Å20 Å25.508 Å2
2---7.756 Å20 Å2
3----7.354 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: final / Resolution: 2.68→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5606 0 0 0 5606
Num. residues----708
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1974SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes956HARMONIC5
X-RAY DIFFRACTIONt_it5722HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion763SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6428SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5722HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg7758HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion1.8
X-RAY DIFFRACTIONt_other_torsion20.85
LS refinement shellResolution: 2.68→2.85 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.1748 18 7.69 %
Rwork0.2285 216 -
all0.2243 234 -
obs--4.51 %
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)
11.022-0.6126-0.73842.52921.05052.22620.00770.01820.0136-0.18680.01370.18430.0334-0.2146-0.02140.1692-0.00020.0503-0.25850.0532-0.2231-5.160814.6689-37.0178
20.44770.49040.63361.76250.99511.37760.02090.030.08620.1799-0.00420.24080.0216-0.0904-0.01680.239-0.01680.0501-0.20710.0377-0.2199-10.75761.5866-18.898
30.17260.3112-1.02873.9938-1.34834.21820.0075-0.0617-0.01650.0453-0.04390.2064-0.0347-0.11650.03640.0610.1262-0.0171-0.0767-0.0071-0.0581-20.6765-31.6625-32.7338
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A109 - 435
2X-RAY DIFFRACTION2{ B|* }B105 - 496
3X-RAY DIFFRACTION3{ D|* }D4 - 69

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