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- PDB-1ydl: Crystal Structure of the Human TFIIH, Northeast Structural Genomi... -

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Basic information

Entry
Database: PDB / ID: 1ydl
TitleCrystal Structure of the Human TFIIH, Northeast Structural Genomics Target HR2045.
Componentsgeneral transcription factor IIH, polypeptide 5
KeywordsTRANSCRIPTION / alpha-beta protein / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


nucleotide-excision repair, preincision complex assembly / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / RNA Polymerase I Transcription Termination / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping ...nucleotide-excision repair, preincision complex assembly / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / RNA Polymerase I Transcription Termination / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / 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 / transcription elongation by RNA polymerase I / 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 / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / RNA Polymerase II Pre-transcription Events / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / cellular response to gamma radiation / 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 / nucleolus / nucleoplasm / cytoplasm
Similarity search - Function
TFB5-like / 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 factor IIH subunit 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsForouhar, F. / Edstrom, W. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Human TFIIH, Northeast Structural Genomics Target HR2045.
Authors: Forouhar, F. / Edstrom, W. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionDec 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 999 SEQUENCE THE FIRST FIVE N-TERMINAL RESIDUES OF THE NATIVE PROTEIN, 1-MVNVL-5, WERE SUBSTITUTED BY ... SEQUENCE THE FIRST FIVE N-TERMINAL RESIDUES OF THE NATIVE PROTEIN, 1-MVNVL-5, WERE SUBSTITUTED BY GTR AND AN N-TAG (MGHHHHHHSH).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: general transcription factor IIH, polypeptide 5


Theoretical massNumber of molelcules
Total (without water)9,2341
Polymers9,2341
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.412, 53.922, 34.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailspossibly dimer

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Components

#1: Protein general transcription factor IIH, polypeptide 5 / TFIIH


Mass: 9234.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C6orf175 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q6ZYL4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.2 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG 3350, 100 mM MgCl2, and 10 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 7, 2004 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→29.25 Å / Num. obs: 6602 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.083 / Net I/σ(I): 22.23
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 5.1 / Num. unique all: 633 / Rsym value: 0.316 / % possible all: 93.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→29.25 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 444155.03 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.297 634 10.7 %RANDOM
Rwork0.236 ---
all0.239 6601 --
obs0.236 5916 88.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.8039 Å2 / ksol: 0.35852 e/Å3
Displacement parametersBiso mean: 35.9 Å2
Baniso -1Baniso -2Baniso -3
1--12.97 Å20 Å20 Å2
2---7.05 Å20 Å2
3---20.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms565 0 0 35 600
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.6
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.282 70 8.9 %
Rwork0.211 715 -
obs-634 70.5 %

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