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- PDB-2mkr: Structural Characterization of a Complex Between the Acidic Trans... -

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Basic information

Entry
Database: PDB / ID: 2mkr
TitleStructural Characterization of a Complex Between the Acidic Transactivation Domain of EBNA2 and the Tfb1/p62 subunit of TFIIH.
Components
  • Epstein-Barr nuclear antigen 2
  • RNA polymerase II transcription factor B subunit 1
KeywordsVIRAL PROTEIN/TRANSCRIPTION / EBV / EBNA2 / TFIIH / TFB1 / ACTIVATION / TRANSCRIPTION / PH DOMAIN / VIRAL PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle progression / host cell nuclear matrix / symbiont-mediated perturbation of host transcription / DNA-templated viral transcription / protein serine/threonine phosphatase inhibitor activity / phosphatidylinositol-5-phosphate binding / symbiont-mediated suppression of host translation initiation / nucleotide-excision repair factor 3 complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIH core complex ...symbiont-mediated perturbation of host cell cycle progression / host cell nuclear matrix / symbiont-mediated perturbation of host transcription / DNA-templated viral transcription / protein serine/threonine phosphatase inhibitor activity / phosphatidylinositol-5-phosphate binding / symbiont-mediated suppression of host translation initiation / nucleotide-excision repair factor 3 complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / TP53 Regulates Transcription of DNA Repair Genes / 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 / RNA Polymerase II Pre-transcription Events / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / Dual incision in TC-NER / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription by RNA polymerase II / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / DNA repair / virus-mediated perturbation of host defense response / host cell nucleus / positive regulation of DNA-templated transcription / nucleus / cytosol
Similarity search - Function
TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like ...TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Epstein-Barr nuclear antigen 2 / General transcription and DNA repair factor IIH subunit TFB1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
Human herpesvirus 4 (Epstein-Barr virus)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 17
AuthorsChabot, P.R. / Raiola, L. / Lussier-Price, M. / Morse, T. / Arseneault, G. / Archambault, J. / Omichinski, J.
CitationJournal: Plos Pathog. / Year: 2014
Title: Structural and Functional Characterization of a Complex between the Acidic Transactivation Domain of EBNA2 and the Tfb1/p62 Subunit of TFIIH.
Authors: Chabot, P.R. / Raiola, L. / Lussier-Price, M. / Morse, T. / Arseneault, G. / Archambault, J. / Omichinski, J.G.
History
DepositionFeb 12, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Derived calculations / Structure summary
Revision 1.2Apr 9, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase II transcription factor B subunit 1
B: Epstein-Barr nuclear antigen 2


Theoretical massNumber of molelcules
Total (without water)14,5372
Polymers14,5372
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 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein RNA polymerase II transcription factor B subunit 1 / General transcription and DNA repair factor IIH subunit TFB1 / TFIIH subunit TFB1 / RNA polymerase ...General transcription and DNA repair factor IIH subunit TFB1 / TFIIH subunit TFB1 / RNA polymerase II transcription factor B 73 kDa subunit / RNA polymerase II transcription factor B p73 subunit


Mass: 12903.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: D9740.3, TFB1, YDR311W / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 / References: UniProt: P32776
#2: Protein/peptide Epstein-Barr nuclear antigen 2 / EBNA-2 / EBV nuclear antigen 2


Mass: 1633.665 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus)
Strain: B95-8 / Gene: BYRF1, EBNA2 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 / References: UniProt: P12978

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1242D 1H-15N HSQC
1332D 1H-13C HSQC
1462D 1H-13C HSQC
1523D 1H-15N NOESY
1653D 1H-15N NOESY
1733D 1H-13C NOESY
1863D 1H-13C NOESY
1962D 1H-13C HSQC aromatic
11063D 1H-13C NOESY aromatic
11133D 1H-13C-12C intermolecular NOESY
11263D 1H-13C-12C intermolecular NOESY
11313D HNCO
11443D HNCO
11513D HN(CA)CB
11643D HN(CA)CB
11713D (H)CCH-TOCSY
11843D (H)CCH-TOCSY
11913D H(CCO)NH
12043D H(CCO)NH
12113D (H)CCH-COSY
12243D (H)CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-13C; U-15N] Tfb1, 2.1 mM EBNA2, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM [U-15N] Tfb1, 2.1 mM EBNA2, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
30.7 mM [U-13C; U-15N] Tfb1, 2.1 mM EBNA2, 20 mM sodium phosphate, 1 mM DTT, 100% D2O100% D2O
40.5 mM [U-13C; U-15N] EBNA2, 1.5 mM Tfb1, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
50.5 mM [U-100% 15N] EBNA2, 1.5 mM Tfb1, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
60.5 mM [U-13C; U-15N] EBNA2, 1.5 mM Tfb1, 20 mM sodium phosphate, 1 mM DTT-24, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMTfb1-1[U-13C; U-15N]1
2.1 mMEBNA2-21
20 mMsodium phosphate-31
1 mMDTT-41
0.7 mMTfb1-5[U-15N]2
2.1 mMEBNA2-62
20 mMsodium phosphate-72
1 mMDTT-82
0.7 mMTfb1-9[U-13C; U-15N]3
2.1 mMEBNA2-103
20 mMsodium phosphate-113
1 mMDTT-123
0.5 mMEBNA2-13[U-13C; U-15N]4
1.5 mMTfb1-144
20 mMsodium phosphate-154
1 mMDTT-164
0.5 mMEBNA2-17[U-100% 15N]5
1.5 mMTfb1-185
20 mMsodium phosphate-195
1 mMDTT-205
0.5 mMEBNA2-21[U-13C; U-15N]6
1.5 mMTfb1-226
20 mMsodium phosphate-236
1 mMDTT-246
Sample conditionsIonic strength: 20 / pH: 6.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CCPNMRCCPNdata analysis
TALOSTALOS-NCornilescu, Delaglio and Baxgeometry optimization
VNMRVariancollection
CNSrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1753 / NOE intraresidue total count: 389 / NOE long range total count: 419 / NOE medium range total count: 517 / NOE sequential total count: 379 / Protein phi angle constraints total count: 74 / Protein psi angle constraints total count: 71
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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