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- PDB-2phe: Model for VP16 binding to PC4 -

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Basic information

Entry
Database: PDB / ID: 2phe
TitleModel for VP16 binding to PC4
Components
  • Alpha trans-inducing protein
  • TRANSCRIPTIONAL COACTIVATOR PC4
KeywordsTRANSCRIPTION / PC4 / VP16 / cofactor / activator
Function / homology
Function and homology information


replication compartment / negative regulation of DNA metabolic process / negative regulation of DNA duplex unwinding / regulation of viral transcription / DNA-templated viral transcription / RNA polymerase II promoter clearance / viral tegument / biological process involved in interaction with host / host cell cytoplasmic vesicle / positive regulation of transcription initiation by RNA polymerase II ...replication compartment / negative regulation of DNA metabolic process / negative regulation of DNA duplex unwinding / regulation of viral transcription / DNA-templated viral transcription / RNA polymerase II promoter clearance / viral tegument / biological process involved in interaction with host / host cell cytoplasmic vesicle / positive regulation of transcription initiation by RNA polymerase II / core promoter sequence-specific DNA binding / molecular function activator activity / single-stranded DNA binding / protein-containing complex assembly / DNA-binding transcription factor binding / transcription regulator complex / host cell cytoplasm / structural constituent of virion / transcription coactivator activity / host cell perinuclear region of cytoplasm / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / host cell nucleus / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / 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) / RNA polymerase II transcriptional coactivator Sub1/Tcp4-like / Transcriptional coactivator p15 (PC4), C-terminal / Transcriptional Coactivator p15 (PC4) / Transcriptional Coactivator Pc4; Chain A ...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) / RNA polymerase II transcriptional coactivator Sub1/Tcp4-like / Transcriptional coactivator p15 (PC4), C-terminal / Transcriptional Coactivator p15 (PC4) / Transcriptional Coactivator Pc4; Chain A / ssDNA-binding transcriptional regulator / Transcriptional Co-activator pc4; Chain A / Roll / Mainly Beta
Similarity search - Domain/homology
Tegument protein VP16 / Activated RNA polymerase II transcriptional coactivator p15
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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
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: TRANSCRIPTIONAL COACTIVATOR PC4
B: TRANSCRIPTIONAL COACTIVATOR PC4
C: Alpha trans-inducing protein


Theoretical massNumber of molelcules
Total (without water)18,4743
Polymers18,4743
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 TRANSCRIPTIONAL COACTIVATOR PC4 / SUB1 homolog / Positive cofactor 4 / P15 / p14


Mass: 7784.024 Da / Num. of mol.: 2 / Fragment: c-terminal core domain / Mutation: N61A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUB1, PC4, RPO2TC1 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P53999
#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 experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-HSQCs
22213C-HN(CA)CB
13113C-HNCO
24215N-NOESY-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2 mM VP16ad U-15N or U15N,13C, 0-0.5 mM PC4 or PC4ctd, 50 or 400 mM KCl, 50 mM phosphate buffer pH 5.6, 2 M D6-Glycine, H2OH2O
20.2 mM PC4 or PC4ctd U-15N, 0-0.5 mM VP16ad, 50 or 400 mM KCl, 50 mM phosphate buffer pH 5.6, 2 M D6-Glycine, H2OH2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100-450 mM 5.6 1 atm298 K
2100-450 mM 5.6 1 atm305 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 PC4 was taken from the PDB entry 1PCF.
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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