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- PDB-2rnq: Solution structure of the C-terminal acidic domain of TFIIE alpha -

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Basic information

Entry
Database: PDB / ID: 2rnq
TitleSolution structure of the C-terminal acidic domain of TFIIE alpha
ComponentsTranscription initiation factor IIE subunit alpha
KeywordsTRANSCRIPTION / general transcription factor / human TFIIE alpha / human TFIIH p62 / acidic domain / PH domain
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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription initiation factor IIE subunit alpha


Theoretical massNumber of molelcules
Total (without water)7,3831
Polymers7,3831
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

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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 doman, 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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1422D DQF-COSY
1522D 1H-1H TOCSY
1622D 1H-1H NOESY
1732D 1H-15N HSQC
1833D 1H-15N TOCSY
1933D 1H-15N NOESY
11043D HN(CA)CB
11143D CBCA(CO)NH
11243D HNCO
11343D C(CO)NH
11443D H(CCO)NH
11543D HNHB
11643D HNHA
11752D 1H-13C HSQC
11853D (H)CCH-TOCSY
11953D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11-2mM TFIIE-ALPHA, 90% H2O/10% D2O90% H2O/10% D2O
21-2mM TFIIE-ALPHA, 100% D2O100% D2O
31-2mM [U-100% 15N] TFIIE-ALPHA, 90% H2O/10% D2O90% H2O/10% D2O
41-2mM [U-100% 13C; U-100% 15N] TFIIE-ALPHA, 90% H2O/10% D2O90% H2O/10% D2O
51-2mM [U-100% 13C; U-100% 15N] TFIIE-ALPHA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 %D2O[U-2H]1
100 %D2O[U-2H]2
Sample conditionsIonic strength: 0 / pH: 6.5 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE5002

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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

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