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- PDB-2phg: Model for VP16 binding to TFIIB -

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Basic information

Entry
Database: PDB / ID: 2phg
TitleModel for VP16 binding to TFIIB
Components
  • Alpha trans-inducing protein
  • Transcription initiation factor IIB
KeywordsTRANSCRIPTION / TF2B / VP16 / activator
Function / homology
Function and homology information


replication compartment / regulation of viral transcription / DNA-templated viral transcription / positive regulation of core promoter binding / viral tegument / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / biological process involved in interaction with host / transcriptional start site selection at RNA polymerase II promoter / host cell cytoplasmic vesicle ...replication compartment / regulation of viral transcription / DNA-templated viral transcription / positive regulation of core promoter binding / viral tegument / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / biological process involved in interaction with host / transcriptional start site selection at RNA polymerase II promoter / host cell cytoplasmic vesicle / germinal vesicle / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / protein acetylation / cell division site / acetyltransferase activity / 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 / viral transcription / RNA polymerase II complex binding / RNA polymerase II transcribes snRNA genes / histone acetyltransferase activity / RNA polymerase II core promoter sequence-specific DNA binding / core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / spindle assembly / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / molecular function activator activity / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin binding / DNA-templated transcription initiation / protein-DNA complex / kinetochore / RNA polymerase II transcription regulator complex / chromosome / protein-containing complex assembly / transcription regulator complex / DNA-binding transcription factor binding / structural constituent of virion / transcription by RNA polymerase II / host cell cytoplasm / transcription coactivator activity / host cell perinuclear region of cytoplasm / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / host cell nucleus / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Alpha trans-inducing protein (Alpha-TIF) / Herpes simplex virus, Tegument protein VP16, C-terminal / Alpha trans-inducing (Alpha-TIF) superfamily / Alpha trans-inducing protein (Alpha-TIF) / Herpes simplex virus virion protein 16 C terminal / Alpha trans-inducing protein (Alpha-TIF) / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. ...Alpha trans-inducing protein (Alpha-TIF) / Herpes simplex virus, Tegument protein VP16, C-terminal / Alpha trans-inducing (Alpha-TIF) superfamily / Alpha trans-inducing protein (Alpha-TIF) / Herpes simplex virus virion protein 16 C terminal / Alpha trans-inducing protein (Alpha-TIF) / 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
Tegument protein VP16 / Transcription initiation factor IIB
Similarity search - Component
Biological speciesHomo sapiens (human)
Herpes simplex virus
MethodSOLUTION NMR / The model was calculated using HADDOCK
AuthorsJonker, H.R.A. / Wechselberger, R.W. / Boelens, R. / Folkers, G.E. / Kaptein, R.
CitationJournal: Biochemistry / Year: 2005
Title: Structural Properties of the Promiscuous VP16 Activation Domain
Authors: Jonker, H.R.A. / Wechselberger, R.W. / Boelens, R. / Folkers, G.E. / Kaptein, R.
History
DepositionApr 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE Residues 4-111 chain A are deleted and S3 is renumbered to S111.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription initiation factor IIB
B: Alpha trans-inducing protein


Theoretical massNumber of molelcules
Total (without water)25,9022
Polymers25,9022
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)10 / 200Top-ranked ensemble, according to the average interaction energy and buried surface area
RepresentativeModel #1lowest energy

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Components

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


Mass: 22995.832 Da / Num. of mol.: 1 / Fragment: c-terminal core domain / Mutation: D111S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2B, TF2B, TFIIB / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q00403
#2: Protein/peptide Alpha trans-inducing protein / Vmw65 / ICP25 / VP16 protein / Alpha- TIF


Mass: 2906.115 Da / Num. of mol.: 1 / Fragment: part of activation domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herpes simplex virus (type 1 / strain 17)
Genus: Simplexvirus / Species: Human herpesvirus 1 / Strain: 17 / Gene: UL48 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P06492

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 15N-HSQCs

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Sample preparation

DetailsContents: 0.2 mM VP16ad U-15N, 0-0.2 mM TFIIBc, 50 mM KCl, 50 mM phosphate buffer pH 5.6, 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 100 mM / pH: 5.6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE7503
Varian INOVAVarianINOVA5004
Varian INOVAVarianINOVA7505

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.xBruker Biospincollection
VNMR1Varian Inc.collection
NMRPipe2.4Delaglio et al.processing
Sparky3.11Goddard et al.data analysis
CNS1.1Brunger et al.structure solution
HADDOCK1.2Dominguez et al.refinement
RefinementMethod: The model was calculated using HADDOCK / Software ordinal: 1
Details: The structure represents a docking model. The starting structure for TFIIB was taken from the PDB entry 1TFB.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Top-ranked ensemble, according to the average interaction energy and buried surface area
Conformers calculated total number: 200 / Conformers submitted total number: 10

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