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- PDB-1z60: Solution structure of the carboxy-terminal domain of human TFIIH ... -

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Basic information

Entry
Database: PDB / ID: 1z60
TitleSolution structure of the carboxy-terminal domain of human TFIIH P44 subunit
ComponentsTFIIH basal transcription factor complex p44 subunit
KeywordsTRANSCRIPTION / Basic transcription factor / zinc binding protein / ring finger
Function / homology
Function and homology information


core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / G protein-coupled receptor internalization / 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 / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex ...core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / G protein-coupled receptor internalization / 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 / RNA polymerase II general transcription initiation factor activity / 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 / 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 / response to UV / 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 / 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 / nuclear speck / regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / Zinc/RING finger domain, C3HC4 (zinc finger) / C1-like domain superfamily / Herpes Virus-1 / von Willebrand factor (vWF) type A domain ...TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / Zinc/RING finger domain, C3HC4 (zinc finger) / C1-like domain superfamily / Herpes Virus-1 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
General transcription factor IIH subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKellenberger, E. / Dominguez, C. / Fribourg, S. / Wasielewski, E. / Moras, D. / Poterszman, A. / Boelens, R. / Kieffer, B.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Solution structure of the C-terminal domain of TFIIH P44 subunit reveals a novel type of C4C4 ring domain involved in protein-protein interactions.
Authors: Kellenberger, E. / Dominguez, C. / Fribourg, S. / Wasielewski, E. / Moras, D. / Poterszman, A. / Boelens, R. / Kieffer, B.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: Structural characterization of the cysteine-rich domain of TFIIH p44 subunit
Authors: Fribourg, S. / Kellenberger, E. / Rogniaux, H. / Poterszman, A. / Van Dorsselaer, A. / Thierry, J.C. / Egly, J.M. / Moras, D. / Kieffer, B.
History
DepositionMar 21, 2005Deposition site: RCSB / Processing site: PDBJ
SupersessionApr 12, 2005ID: 1E53
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TFIIH basal transcription factor complex p44 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8263
Polymers6,6961
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1the best geometry

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Components

#1: Protein TFIIH basal transcription factor complex p44 subunit / TFIIH P44 SUBUNIT / Basic transcription factor 2 44 kDa subunit / BTF2-p44 / General transcription ...TFIIH P44 SUBUNIT / Basic transcription factor 2 44 kDa subunit / BTF2-p44 / General transcription factor IIH polypeptide 2


Mass: 6695.528 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN / Mutation: C381S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13888
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-edited TOCSY and NOESY
2213D 15N-edited TOCSY and NOESY
2322D TOCSY and NOESY
141HSQC
NMR detailsText: 113Cd-1H HSQC spectrum was recorded using a broadband z-gradient probe at 293 K

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM p44 U-15N; 20mM deuterated TrisHCl buffer, 20mM NaCl and 0.5mM DTT90% H2O/10% D2O
20.5mM p44; 20mM deuterated TrisHCl buffer, 20mM NaCl and 0.5mM DTT90% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17 ambient 293 K
27 ambient 303 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA / CNS1.2.Nilgesstructure solution
XPLOR-NIH2.0.6refinement
XEASY1.2Bartelsdata analysis
XwinNMR2.6brukerprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Automated assignment of the NOE was performed, The structures are based on 1294 unambiguous NOE-derived distance constraints, 32 dihedral angle restraints and 17 distance restraints from ...Details: Automated assignment of the NOE was performed, The structures are based on 1294 unambiguous NOE-derived distance constraints, 32 dihedral angle restraints and 17 distance restraints from hydrogen bonds. Geometry of the zinc binding site II is distorded due to conformational exchange averaging.
NMR representativeSelection criteria: the best geometry
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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