[English] 日本語
Yorodumi
- PDB-5o85: p34-p44 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5o85
Titlep34-p44 complex
Components
  • General transcription factor IIH subunit 2
  • General transcription factor IIH subunit 3
KeywordsTRANSCRIPTION / DNA repair / TFIIH / TFIIH interaction network / p34-p44 complex
Function / homology
Function and homology information


core TFIIH complex portion of holo TFIIH complex / G protein-coupled receptor internalization / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / RNA Polymerase I Transcription Termination / transcription preinitiation complex / 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 ...core TFIIH complex portion of holo TFIIH complex / G protein-coupled receptor internalization / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / RNA Polymerase I Transcription Termination / transcription preinitiation complex / 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 / RNA polymerase II general transcription initiation factor activity / 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 / TP53 Regulates Transcription of DNA Repair Genes / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / NoRC negatively regulates rRNA expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / 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 / DNA repair / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / 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 ...TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / 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 / General transcription factor IIH subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsRadu, L. / Poterszman, A.
Funding support France, 5items
OrganizationGrant numberCountry
French National Research AgencyANR-12-BSV8-0015-01 France
INCAINCA_9378 France
Association pour la Recherche sur le CancerSL120120304592 France
La ligue contre le cancerCCIR-GE 2013 and Post-doctoral fellowship to L.R. France
French National Research AgencyANR-10-INSB-05-01 France
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: The intricate network between the p34 and p44 subunits is central to the activity of the transcription/DNA repair factor TFIIH.
Authors: Radu, L. / Schoenwetter, E. / Braun, C. / Marcoux, J. / Koelmel, W. / Schmitt, D.R. / Kuper, J. / Cianferani, S. / Egly, J.M. / Poterszman, A. / Kisker, C.
History
DepositionJun 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.3Jan 17, 2024Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: General transcription factor IIH subunit 3
B: General transcription factor IIH subunit 2
C: General transcription factor IIH subunit 3
D: General transcription factor IIH subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,0268
Polymers157,7644
Non-polymers2624
Water00
1
A: General transcription factor IIH subunit 3
B: General transcription factor IIH subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0134
Polymers78,8822
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: General transcription factor IIH subunit 3
D: General transcription factor IIH subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0134
Polymers78,8822
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.407, 120.388, 128.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

-
Components

#1: Protein General transcription factor IIH subunit 3 / Basic transcription factor 2 34 kDa subunit / BTF2 p34 / General transcription factor IIH ...Basic transcription factor 2 34 kDa subunit / BTF2 p34 / General transcription factor IIH polypeptide 3 / TFIIH basal transcription factor complex p34 subunit


Mass: 34416.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13889
#2: Protein General transcription factor IIH subunit 2 / Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH ...Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH polypeptide 2 / TFIIH basal transcription factor complex p44 subunit


Mass: 44465.934 Da / Num. of mol.: 2 / Mutation: C381S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H2, BTF2P44 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13888
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 mM Tris-HCl or Hepes (pH 7.0 to 8.5) and 20-40% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.28236 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28236 Å / Relative weight: 1
ReflectionResolution: 3.19→46.55 Å / Num. obs: 141682 / % possible obs: 99.4 % / Redundancy: 13.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.061 / Net I/σ(I): 8.9
Reflection shellResolution: 3.19→3.39 Å / Redundancy: 12.8 % / Rmerge(I) obs: 3.092 / Mean I/σ(I) obs: 1 / Num. unique all: 19316 / CC1/2: 0.593 / Rpim(I) all: 1.272 / % possible all: 96.4

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4pn7

4pn7


Resolution: 3.4→40.7 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 38.54
RfactorNum. reflection% reflectionSelection details
Rfree0.29 445 4.94 %Random selection
Rwork0.24 ---
obs0.233 9015 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.4→40.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3845 0 4 0 3849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033912
X-RAY DIFFRACTIONf_angle_d0.6265283
X-RAY DIFFRACTIONf_dihedral_angle_d15.4072364
X-RAY DIFFRACTIONf_chiral_restr0.043620
X-RAY DIFFRACTIONf_plane_restr0.004663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4002-3.8920.39361510.33452807X-RAY DIFFRACTION100
3.892-4.90250.28781470.22852816X-RAY DIFFRACTION100
4.9025-43.95880.26391470.20832947X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more