[English] 日本語
Yorodumi
- PDB-2jtx: NMR structure of the TFIIE-alpha carboxyl terminus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jtx
TitleNMR structure of the TFIIE-alpha carboxyl terminus
ComponentsTranscription initiation factor IIE subunit alpha
KeywordsTRANSCRIPTION / TFIIE / TFIIH / activation domains / p53 / Transcription regulation
Function / homology
Function and homology information


transcription factor TFIIE complex / transcription open complex formation at RNA polymerase II promoter / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / 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 ...transcription factor TFIIE complex / transcription open complex formation at RNA polymerase II promoter / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / 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 II transcribes snRNA genes / RNA Polymerase II Pre-transcription Events / transcription initiation at RNA polymerase II promoter / transcription by RNA polymerase II / molecular adaptor activity / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
Helix Hairpins - #1250 / Transcription factor TFIIE alpha subunit, C-terminal / C-terminal general transcription factor TFIIE alpha / 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 ...Helix Hairpins - #1250 / Transcription factor TFIIE alpha subunit, C-terminal / C-terminal general transcription factor TFIIE alpha / 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 / Helix Hairpins / Helix non-globular / Special / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
General transcription factor IIE subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsDi Lello, P. / Omichinski, J.G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: p53 and TFIIEalpha share a common binding site on the Tfb1/p62 subunit of TFIIH.
Authors: Di Lello, P. / Miller Jenkins, L.M. / Mas, C. / Langlois, C. / Malitskaya, E. / Fradet-Turcotte, A. / Archambault, J. / Legault, P. / Omichinski, J.G.
History
DepositionAug 8, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999sequence Author's sequence reflects the S->D conflict of residue 352 between different references, ...sequence Author's sequence reflects the S->D conflict of residue 352 between different references, as indicated in UNP entry P29083.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription initiation factor IIE subunit alpha


Theoretical massNumber of molelcules
Total (without water)11,4931
Polymers11,4931
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 / 50structures 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: 11493.229 Da / Num. of mol.: 1 / Fragment: carboxyl terminus, residues 336-439
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2E1, TF2E1 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P29083

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1223D HNHA
1323D 1H-15N NOESY
1433D HNCO
1533D HN(CA)CB
1633D CBCA(CO)NH
1733D C(CO)NH
1833D H(CCO)NH
1943D (H)CCH-COSY
11043D 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM TFIIE-alpha;, 20 mM sodium phosphate, 200 mM sodium chloride, 1 mM EDTA, 100% D2O100% D2O
21 mM [U-100% 15N] TFIIE-alpha;, 20 mM sodium phosphate, 200 mM sodium chloride, 1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 13C; U-100% 15N] TFIIE-alpha;, 20 mM sodium phosphate, 200 mM sodium chloride, 1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-100% 13C; U-100% 15N] TFIIE-alpha;, 20 mM sodium phosphate, 200 mM sodium chloride, 1 mM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTFIIE-alpha;1
20 mMsodium phosphate1
200 mMsodium chloride1
1 mMEDTA1
1 mMTFIIE-alpha;[U-100% 15N]2
20 mMsodium phosphate2
200 mMsodium chloride2
1 mMEDTA2
1 mMTFIIE-alpha;[U-100% 13C; U-100% 15N]3
20 mMsodium phosphate3
200 mMsodium chloride3
1 mMEDTA3
1 mMTFIIE-alpha;[U-100% 13C; U-100% 15N]4
20 mMsodium phosphate4
200 mMsodium chloride4
1 mMEDTA4
Sample conditionsIonic strength: 0.2 / pH: 7.5 / Pressure: ambient / Temperature: 300 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityVarianUNITY5001
Varian UnityVarianUNITY6002
Varian UnityVarianUNITY8003

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1.CVariancollection
NMRPipe2.2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / 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