[English] 日本語
Yorodumi
- PDB-2jnj: Solution structure of the p8 TFIIH subunit -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jnj
TitleSolution structure of the p8 TFIIH subunit
ComponentsTFIIH basal transcription factor complex TTD-A subunit
KeywordsTRANSCRIPTION / protein / Structural Genomics / Structural Proteomics in Europe 2 / SPINE-2
Function / homology
Function and homology information


nucleotide-excision repair, preincision complex assembly / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / RNA Polymerase I Transcription Termination / transcription factor TFIID complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / 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 core complex / transcription factor TFIIH holo complex / RNA Polymerase I Transcription Termination / transcription factor TFIID complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / 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 / transcription elongation by RNA polymerase I / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / 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)
MethodSOLUTION NMR / simulated annealing
AuthorsVitorino, M. / Atkinson, R.A. / Moras, D. / Poterszman, A. / Kieffer, B. / Structural Proteomics in Europe 2 (SPINE-2)
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Solution Structure and Self-association Properties of the p8 TFIIH Subunit Responsible for Trichothiodystrophy
Authors: Vitorino, M. / Coin, F. / Zlobinskaya, O. / Atkinson, R.A. / Moras, D. / Egly, J.M. / Poterszman, A. / Kieffer, B.
History
DepositionJan 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.SG_entry / _pdbx_nmr_software.name / _struct_keywords.text / _struct_ref_seq_dif.details
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TFIIH basal transcription factor complex TTD-A subunit
B: TFIIH basal transcription factor complex TTD-A subunit


Theoretical massNumber of molelcules
Total (without water)16,6852
Polymers16,6852
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein TFIIH basal transcription factor complex TTD-A subunit / General transcription factor IIH polypeptide 5 / TFB5 ortholog


Mass: 8342.638 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H5, TTDA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q6ZYL4

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1212D 1H-13C HSQC
1322D 1H-1H TOCSY
1422D 1H-1H NOESY
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D HN(CO)CA
1913D (H)CCH-TOCSY
11013D (H)CCH-COSY
11133D 1H-15N NOESY
11233D 1H-15N TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
1300 uM [U-99% 13C, U-99% 15N] protein, 2.5 mM beta-mercaptoethanol, 50 mM sodium chloride, 10 mM TRIS, 90% H2O/10% D2O90% H2O/10% D2O
2300 uM protein, 2.5 mM beta-mercaptoethanol, 50 mM sodium chloride, 10 mM TRIS, 90% H2O/10% D2O90% H2O/10% D2O
3300 uM [U-99% 15N] protein, 2.5 mM beta-mercaptoethanol, 50 mM sodium chloride, 10 mM TRIS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMentity[U-99% 13C; U-99% 15N]1
2.5 mMbeta-mercaptoethanol1
50 mMsodium chloride1
10 mMTRIS1
300 uMentity2
2.5 mMbeta-mercaptoethanol2
50 mMsodium chloride2
10 mMTRIS2
300 uMentity[U-99% 15N]3
2.5 mMbeta-mercaptoethanol3
50 mMsodium chloride3
10 mMTRIS3
Sample conditionsIonic strength: 50 / pH: 7 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

-
Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
XEASYBartels et al.peak picking
ARIALinge, O'Donoghue and Nilgeschemical shift assignment
TALOSCornilescu, Delaglio and Baxgeometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: NMR WaterRefine Protocol
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 10

+
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