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- PDB-1tfb: NMR STUDIES OF HUMAN GENERAL TRANSCRIPTION FACTOR TFIIB: DYNAMICS... -

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Entry
Database: PDB / ID: 1tfb
TitleNMR STUDIES OF HUMAN GENERAL TRANSCRIPTION FACTOR TFIIB: DYNAMICS AND INTERACTION WITH VP16 ACTIVATION DOMAIN, 20 STRUCTURES
ComponentsTFIIB
KeywordsTRANSCRIPTION FACTOR / HUMAN GENERAL TRANSCRIPTION FACTOR TFIIB / C-TERMINAL CORE DOMAIN / CYCLIN BOX FOLD
Function / homology
Function and homology information


positive regulation of core promoter binding / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / transcriptional start site selection at RNA polymerase II promoter / germinal vesicle / nuclear thyroid hormone receptor binding / transcription preinitiation complex / protein acetylation / cell division site / RNA polymerase II general transcription initiation factor activity ...positive regulation of core promoter binding / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / transcriptional start site selection at RNA polymerase II promoter / germinal vesicle / nuclear thyroid hormone receptor binding / transcription preinitiation complex / protein acetylation / cell division site / 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 / acetyltransferase activity / RNA polymerase II complex binding / viral transcription / RNA polymerase II transcribes snRNA genes / RNA polymerase II core promoter sequence-specific DNA binding / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / RNA polymerase II preinitiation complex assembly / spindle assembly / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / promoter-specific chromatin binding / protein-DNA complex / kinetochore / RNA polymerase II transcription regulator complex / chromosome / DNA-binding transcription factor binding / transcription by RNA polymerase II / nuclear body / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Cyclin-like / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / TFIIB zinc-binding / Cyclin A; domain 1 ...Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Cyclin-like / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / TFIIB zinc-binding / Cyclin A; domain 1 / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription initiation factor IIB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsBagby, S. / Ikura, M.
Citation
Journal: Biochemistry / Year: 1998
Title: Human general transcription factor TFIIB: conformational variability and interaction with VP16 activation domain.
Authors: Hayashi, F. / Ishima, R. / Liu, D. / Tong, K.I. / Kim, S. / Reinberg, D. / Bagby, S. / Ikura, M.
#1: Journal: Nature / Year: 1995
Title: Crystal Structure of a TFIIB-TBP-TATA-Element Ternary Complex
Authors: Nikolov, D.B. / Chen, H. / Halay, E.D. / Usheva, A.A. / Hisatake, K. / Lee, D.K. / Roeder, R.G. / Burley, S.K.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1995
Title: Solution Structure of the C-Terminal Core Domain of Human TFIIB: Similarity to Cyclin a and Interaction with TATA-Binding Protein
Authors: Bagby, S. / Kim, S. / Maldonado, E. / Tong, K.I. / Reinberg, D. / Ikura, M.
History
DepositionNov 14, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TFIIB


Theoretical massNumber of molelcules
Total (without water)23,1981
Polymers23,1981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

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Components

#1: Protein TFIIB


Mass: 23198.107 Da / Num. of mol.: 1
Fragment: CONSTRUCT COMPRISES RESIDUES 1 - 3 AND 112 - 316 OF FULL LENGTH HUMAN TFIIB
Mutation: DEL(4 - 111)
Source method: isolated from a genetically manipulated source
Details: RESIDUES MET 1 AND ALA 2 ARE OMITTED FROM THE COORDINATES, AND SER 3 IS NUMBERED AS SER 111
Source: (gene. exp.) Homo sapiens (human)
Description: FURTHER DETAILS CAN BE FOUND IN HA ET AL., GENES AND DEVELOPMENT 7 (1993) 1021
Cell line: BL21 / Gene: HUMAN TFIIB DELTA 4-111 / Plasmid: PET11A / Species (production host): Escherichia coli / Gene (production host): HUMAN TFIIB DELTA 4-111 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q00403

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 20

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