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- PDB-1dl6: SOLUTION STRUCTURE OF HUMAN TFIIB N-TERMINAL DOMAIN -

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Entry
Database: PDB / ID: 1dl6
TitleSOLUTION STRUCTURE OF HUMAN TFIIB N-TERMINAL DOMAIN
ComponentsTRANSCRIPTION FACTOR II B (TFIIB)
KeywordsGENE REGULATION / ZINC RIBBON
Function / homology
Function and homology information


positive regulation of core promoter binding / meiotic sister chromatid cohesion / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase II core complex assembly / germinal vesicle / transcription preinitiation complex / nuclear thyroid hormone receptor binding / protein acetylation / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape ...positive regulation of core promoter binding / meiotic sister chromatid cohesion / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase II core complex assembly / germinal vesicle / transcription preinitiation complex / nuclear thyroid hormone receptor binding / protein acetylation / 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 / cell division site / RNA polymerase II complex binding / viral transcription / acetyltransferase activity / RNA polymerase II transcribes snRNA genes / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / RNA polymerase II core promoter sequence-specific DNA binding / spindle assembly / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / promoter-specific chromatin binding / protein-DNA complex / transcription initiation at RNA polymerase II promoter / 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
N-terminal domain of TfIIb - #10 / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Zinc finger, TFIIB-type / TFIIB zinc-binding / N-terminal domain of TfIIb ...N-terminal domain of TfIIb - #10 / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Zinc finger, TFIIB-type / TFIIB zinc-binding / N-terminal domain of TfIIb / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Transcription initiation factor IIB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING TORSION ANGLE DYNAMICS
AuthorsChen, H.-T. / Legault, P. / Glushka, J. / Omichinski, J.G. / Scott, R.A.
CitationJournal: Protein Sci. / Year: 2000
Title: Structure of a (Cys3His) zinc ribbon, a ubiquitous motif in archaeal and eucaryal transcription.
Authors: Chen, H.T. / Legault, P. / Glushka, J. / Omichinski, J.G. / Scott, R.A.
History
DepositionDec 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: TRANSCRIPTION FACTOR II B (TFIIB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4352
Polymers6,3691
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 29structures with the lowest energy
RepresentativeModel #15closest to the average

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Components

#1: Protein TRANSCRIPTION FACTOR II B (TFIIB)


Mass: 6369.143 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / References: UniProt: Q00403
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 15N-SEPARATED NOESY

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Sample preparation

DetailsContents: 3MM HTFIIB N-TERMINAL DOMAIN U-15N; 50MM PHOSPHATE; 90% H2O, 10% D2O
Sample conditionspH: 7.0 / Pressure: AMBIENT / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1VARIAN ASSOCIATES, INC.collection
NMRPipe1.7DELAGLIOprocessing
NMRDraw1.7DELAGLIOdata analysis
CNS0.4BRUNGERrefinement
RefinementMethod: DISTANCE GEOMETRY SIMULATED ANNEALING TORSION ANGLE DYNAMICS
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 443 RESTRAINTS, 431 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 12 DISTANCE RESTRAINTS FROM HYDROGEN BONDS.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 29 / Conformers submitted total number: 25

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