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- PDB-1ro4: RDC-derived models of the zinc ribbon domain of human general tra... -

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Basic information

Entry
Database: PDB / ID: 1ro4
TitleRDC-derived models of the zinc ribbon domain of human general transcription factor TFIIB (zinc free structures)
ComponentsTranscription initiation factor IIB
KeywordsMETAL BINDING PROTEIN / Zinc ribbon / Rubredoxin knuckle
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 / spindle assembly / RNA polymerase II core promoter sequence-specific DNA binding / 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 / transcription initiation at RNA polymerase II promoter / 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
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 / simulated annealing
AuthorsGhosh, M. / Ikura, M.
CitationJournal: Biochem.J. / Year: 2004
Title: Probing Zn2+-binding effects on the zinc-ribbon domain of human general transcription factor TFIIB.
Authors: Ghosh, M. / Elsby, L.M. / Mal, T.K. / Gooding, J.M. / Roberts, S.G. / Ikura, M.
History
DepositionDec 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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
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 initiation factor IIB


Theoretical massNumber of molelcules
Total (without water)6,5711
Polymers6,5711
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)35 / 35structures with the least restraint violations, structures with the lowest energy
Representative

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Components

#1: Protein Transcription initiation factor IIB / General transcription factor TFIIB / S300-II


Mass: 6571.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2B, TFIIB, TF2B / Plasmid: pET11B / Species (production host): Escherichia coli / 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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N IPAP HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6mM TFIIB Uniform labeling with 15N: U-98% 15N, 20mM [2H4]-imidazole hydrochloride, 5% glycerol and 20mM sodium sulfate at pH 6.5, 95% H2O/5% D2O95% H2O/5% D2O
20.6mM TFIIB Uniform labeling with 15N: U-98% 15N, 20mM [2H4]-imidazole hydrochloride, 5% glycerol and 20mM sodium sulfate at pH 6.5, 12mg/mL of filamentous phage, Pf1, 95% H2O/5% D2O95% H2O/5% D2O
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe2.1Frank Delaglioprocessing
NMRView5Bruce A. Johnsondata analysis
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 465 restraints, 443 are distance constraints, 22 1H-15N RDC restraints
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 35 / Conformers submitted total number: 35

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