[English] 日本語
Yorodumi
- PDB-2rnr: Solution structure of the complex between TFIIE alpha C-terminal ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rnr
TitleSolution structure of the complex between TFIIE alpha C-terminal acidic domain and TFIIH p62 PH domain
Components
  • TFIIH basal transcription factor complex p62 subunit
  • Transcription initiation factor IIE subunit alpha
KeywordsTRANSCRIPTION / general transcription factor / human TFIIE alpha / human TFIIH p62 / acidic domain / PH domain / DNA DAMAGE / DNA REPAIR
Function / homology
Function and homology information


transcription factor TFIIE complex / transcription open complex formation at RNA polymerase II promoter / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / nuclear thyroid hormone receptor binding / 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 ...transcription factor TFIIE complex / transcription open complex formation at RNA polymerase II promoter / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / nuclear thyroid hormone receptor binding / 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 / regulation of cyclin-dependent protein serine/threonine kinase activity / RNA Polymerase I Transcription Initiation / RNA polymerase II transcribes snRNA genes / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / transcription 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 / hormone-mediated signaling pathway / 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 / molecular adaptor activity / DNA repair / chromatin binding / positive regulation of DNA-templated transcription / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
Transcription factor TFIIE alpha subunit, C-terminal / C-terminal general transcription factor TFIIE alpha / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins ...Transcription factor TFIIE alpha subunit, C-terminal / C-terminal general transcription factor TFIIE alpha / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription factor E / TFIIE alpha subunit / TFE/IIEalpha-type HTH domain profile. / Transcription initiation factor IIE / Zinc finger, TFIIB-type / TFIIB zinc-binding / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
General transcription factor IIE subunit 1 / General transcription factor IIH subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, simulated annealing
AuthorsOkuda, M. / Nishimura, Y.
CitationJournal: Embo J. / Year: 2008
Title: Structural insight into the TFIIE-TFIIH interaction: TFIIE and p53 share the binding region on TFIIH
Authors: Okuda, M. / Tanaka, A. / Satoh, M. / Mizuta, S. / Takazawa, M. / Ohkuma, Y. / Nishimura, Y.
History
DepositionJan 31, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription initiation factor IIE subunit alpha
B: TFIIH basal transcription factor complex p62 subunit


Theoretical massNumber of molelcules
Total (without water)19,8332
Polymers19,8332
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Transcription initiation factor IIE subunit alpha / TFIIE-alpha / General transcription factor IIE subunit 1 / General transcription factor IIE 56 kDa subunit


Mass: 7382.924 Da / Num. of mol.: 1 / Fragment: C-terminal acidic domain, UNP residues 378-439
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P29083
#2: Protein TFIIH basal transcription factor complex p62 subunit / Basic transcription factor 2 62 kDa subunit / BTF2-p62 / General transcription factor IIH polypeptide 1


Mass: 12450.445 Da / Num. of mol.: 1 / Fragment: PH domain, UNP residues 1-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P32780

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1323D HN(CA)CB
1423D CBCA(CO)NH
1523D HN(CO)CA
1623D HNCA
1723D HNCO
1823D HBHA(CO)NH
1923D C(CO)NH
11023D H(CCO)NH
11123D HNHB
11223D 1H-15N NOESY
11323D HNHA
11432D 1H-13C HSQC
11533D (H)CCH-TOCSY
11633D 1H-13C NOESY
11742D 1H-15N HSQC
11843D 1H-15N NOESY
11953D HN(CA)CB
12053D CBCA(CO)NH
12153D HN(CO)CA
12253D HNCA
12353D HNCO
12453D HBHA(CO)NH
12553D C(CO)NH
12653D H(CCO)NH
12753D HNHB
12853D 1H-15N NOESY
12953D HNHA
13062D 1H-13C HSQC
13163D (H)CCH-TOCSY
13263D 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5MM [U-100% 15N] TFIIE-ALPHA, 0.5MM TFIIH P62; 20MM POTASSIUM PHOSPHATE, 5MM [U-99% 2H] DTT, 90% H2O/10% D2O90% H2O/10% D2O
20.5MM [U-100% 13C; U-100% 15N] TFIIE-ALPHA, 0.5MM TFIIH P62; 20MM POTASSIUM PHOSPHATE, 5MM [U-99% 2H] DTT, 90% H2O/10% D2O90% H2O/10% D2O
30.5MM [U-100% 13C; U-100% 15N] TFIIE-ALPHA, 0.5MM TFIIH P62; 20MM POTASSIUM PHOSPHATE, 5MM [U-99% 2H] DTT, 100% D2O100% D2O
40.5MM [U-100% 15N] TFIIH P62, 0.5mM TFIIE-ALPHA; 20MM POTASSIUM PHOSPHATE, 5MM [U-99% 2H] DTT, 90% H2O/10% D2O90% H2O/10% D2O
50.5MM [U-100% 13C; U-100% 15N] TFIIH P62, 0.5MM TFIIE-ALPHA; 20MM POTASSIUM PHOSPHATE, 5MM [U-99% 2H] DTT, 90% H2O/10% D2O90% H2O/10% D2O
60.5MM [U-100% 13C; U-100% 15N] TFIIH P62, 0.5MM TFIIE-ALPHA; 20MM POTASSIUM PHOSPHATE, 5MM [U-99% 2H] DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 %D2O[U-2H]1
20 mMpotassium phosphate1
5 mMDTT[U-99% 2H]1
100 %D2O[U-2H]2
20 mMpotassium phosphate2
5 mMDTT[U-99% 2H]2
Sample conditionsIonic strength: 0 / pH: 6.8 / Pressure: ambient / Temperature: 305 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE5003

-
Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: DGSA-distance geometry simulated annealing, simulated annealing
Software ordinal: 1 / Details: refinement with water
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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