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- PDB-1tba: SOLUTION STRUCTURE OF A TBP-TAFII230 COMPLEX: PROTEIN MIMICRY OF ... -

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Entry
Database: PDB / ID: 1tba
TitleSOLUTION STRUCTURE OF A TBP-TAFII230 COMPLEX: PROTEIN MIMICRY OF THE MINOR GROOVE SURFACE OF THE TATA BOX UNWOUND BY TBP, NMR, 25 STRUCTURES
Components
  • TRANSCRIPTION INITIATION FACTOR IID 230K CHAIN
  • TRANSCRIPTION INITIATION FACTOR TFIID
KeywordsCOMPLEX (TRANSCRIPTION FACTORS) / TBP / TAF / TAFII230 / TFIID / SOLUTION STRUCTURE
Function / homology
Function and homology information


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 Pre-transcription Events / Regulation of TP53 Activity through Phosphorylation / : / : / : / histone H3K14 acetyltransferase activity ...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 Pre-transcription Events / Regulation of TP53 Activity through Phosphorylation / : / : / : / histone H3K14 acetyltransferase activity / ubiquitin activating enzyme activity / PRC1 complex / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase III / histone H4 acetyltransferase activity / RNA polymerase I general transcription initiation factor binding / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / DNA binding, bending / : / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / Estrogen-dependent gene expression / RNA polymerase II general transcription initiation factor activity / 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 TFIID complex / RNA Polymerase II Pre-transcription Events / ubiquitin conjugating enzyme activity / nucleolar large rRNA transcription by RNA polymerase I / transcription factor binding / RNA polymerase II core promoter sequence-specific DNA binding / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / disordered domain specific binding / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine/threonine kinase activity / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Transcription Initiation Factor IId 230k; Chain A / TAFII-230 TBP-binding domain / TATA-Binding Protein / TAFII-230 TBP-binding / Transcription initiation factor TFIID subunit 1, animal / TAFII-230 TBP-binding domain superfamily / TATA box-binding protein binding / Zinc knuckle / Zinc knuckle / Transcription initiation factor TFIID subunit 1, histone acetyltransferase domain ...Transcription Initiation Factor IId 230k; Chain A / TAFII-230 TBP-binding domain / TATA-Binding Protein / TAFII-230 TBP-binding / Transcription initiation factor TFIID subunit 1, animal / TAFII-230 TBP-binding domain superfamily / TATA box-binding protein binding / Zinc knuckle / Zinc knuckle / Transcription initiation factor TFIID subunit 1, histone acetyltransferase domain / Transcription initiation factor TFIID subunit 1 / Protein of unknown function (DUF3591) / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / TATA-box binding protein, eukaryotic / TATA-Binding Protein / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / TBP domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TATA-box-binding protein / Transcription initiation factor TFIID subunit 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Saccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR
AuthorsLiu, D. / Ishima, R. / Tong, K.I. / Bagby, S. / Kokubo, T. / Muhandiram, D.R. / Kay, L.E. / Nakatani, Y. / Ikura, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Solution structure of a TBP-TAF(II)230 complex: protein mimicry of the minor groove surface of the TATA box unwound by TBP.
Authors: Liu, D. / Ishima, R. / Tong, K.I. / Bagby, S. / Kokubo, T. / Muhandiram, D.R. / Kay, L.E. / Nakatani, Y. / Ikura, M.
History
DepositionAug 16, 1998Processing site: BNL
Revision 1.0Aug 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSCRIPTION INITIATION FACTOR IID 230K CHAIN
B: TRANSCRIPTION INITIATION FACTOR TFIID


Theoretical massNumber of molelcules
Total (without water)27,1332
Polymers27,1332
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)25 / -
Representative

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Components

#1: Protein TRANSCRIPTION INITIATION FACTOR IID 230K CHAIN / TAFII230


Mass: 7012.671 Da / Num. of mol.: 1 / Fragment: RESIDUES 11-77
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: P51123
#2: Protein TRANSCRIPTION INITIATION FACTOR TFIID / TBP


Mass: 20120.754 Da / Num. of mol.: 1 / Fragment: CORE DOMAIN RESIDUES 60-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P13393

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE STRUCTURE WAS DETERMINED USING MULTIDIMENSIONAL HETERONUCLEAR NMR ON 13C, 15N AND 2H-LABELED TBP AND TAF

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Sample preparation

Sample conditionspH: 7.0 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR softwareName: X-PLOR / Version: 3.851 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 25

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