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- PDB-1d8j: SOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BETA -

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Basic information

Entry
Database: PDB / ID: 1d8j
TitleSOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BETA
ComponentsGENERAL TRANSCRIPTION FACTOR TFIIE-BETA
KeywordsGENE REGULATION / WINGED HELIX-TURN-HELIX / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


transcription factor TFIIE complex / 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 ...transcription factor TFIIE complex / 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 / DNA binding / RNA binding / nucleoplasm / cytosol
Similarity search - Function
Transcription factor TFIIE beta subunit, DNA-binding domain / Transcription initiation factor TFIIE, beta subunit / TFA2, Winged helix domain 2 / TFIIE beta subunit core domain / TFA2 Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Transcription factor TFIIE beta subunit, DNA-binding domain / Transcription initiation factor TFIIE, beta subunit / TFA2, Winged helix domain 2 / TFIIE beta subunit core domain / TFA2 Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription initiation factor IIE subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / 4D SIMULATED ANNEALING
AuthorsOkuda, M. / Watanabe, Y. / Okamura, H. / Hanaoka, F. / Ohkuma, Y. / Nishimura, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: EMBO J. / Year: 2000
Title: Structure of the central core domain of TFIIEbeta with a novel double-stranded DNA-binding surface.
Authors: Okuda, M. / Watanabe, Y. / Okamura, H. / Hanaoka, F. / Ohkuma, Y. / Nishimura, Y.
History
DepositionOct 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: GENERAL TRANSCRIPTION FACTOR TFIIE-BETA


Theoretical massNumber of molelcules
Total (without water)9,2881
Polymers9,2881
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 least restraint violations
RepresentativeModel #20closest to the average

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Components

#1: Protein GENERAL TRANSCRIPTION FACTOR TFIIE-BETA


Mass: 9287.704 Da / Num. of mol.: 1 / Fragment: CENTRAL CORE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: P29084

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D NOESY
1213D 13C-SEPARATED NOESY
1323D 15N-SEPARATED NOESY
1414D 13C-SEPARATED NOESY
152HNHA
162HMQC-J
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY.

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Sample preparation

Details
Solution-IDContents
11-2MM PROTEIN U-15N,13C; 20MM PHOSPHATE BUFFER, 500MM NACL
31-2MM PROTEIN ; 20MM PHOSPHATE BUFFER, 500MM NACL
Sample conditionsIonic strength: 500mM NACL / pH: 6.0 / Pressure: AMBIENT / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker AMXBrukerAMX5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.6DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER, BAXprocessing
PIPP, CAPP, STAPP3.9GARRETT, POWERS, GRONENBORN, CLOREdata analysis
EMBOSS5NAKAI, KIDERA, NAKAMURAstructure solution
EMBOSS5NAKAI, KIDERA, NAKAMURArefinement
RefinementMethod: 4D SIMULATED ANNEALING / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1224 RESTRAINTS, 1184 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 38 DIHEDRAL ANGLE RESTRAINTS, 40 DISTANCE RESTRAINTS FROM HYDROGEN BONDS.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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