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Yorodumi- PDB-2mkr: Structural Characterization of a Complex Between the Acidic Trans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mkr | ||||||
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Title | Structural Characterization of a Complex Between the Acidic Transactivation Domain of EBNA2 and the Tfb1/p62 subunit of TFIIH. | ||||||
Components |
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Keywords | VIRAL 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 / protein serine/threonine phosphatase inhibitor activity / symbiont-mediated perturbation of host transcription / DNA-templated viral transcription / 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 / protein serine/threonine phosphatase inhibitor activity / symbiont-mediated perturbation of host transcription / DNA-templated viral transcription / 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 innate immune response / 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 | ||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) Human herpesvirus 4 (Epstein-Barr virus) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Model details | closest to the average, model 17 | ||||||
Authors | Chabot, P.R. / Raiola, L. / Lussier-Price, M. / Morse, T. / Arseneault, G. / Archambault, J. / Omichinski, J. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mkr.cif.gz | 787.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mkr.ent.gz | 659.6 KB | Display | PDB format |
PDBx/mmJSON format | 2mkr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mkr_validation.pdf.gz | 553.7 KB | Display | wwPDB validaton report |
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Full document | 2mkr_full_validation.pdf.gz | 889.5 KB | Display | |
Data in XML | 2mkr_validation.xml.gz | 69.6 KB | Display | |
Data in CIF | 2mkr_validation.cif.gz | 83.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/2mkr ftp://data.pdbj.org/pub/pdb/validation_reports/mk/2mkr | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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#2: Protein/peptide | 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 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 20 / pH: 6.5 / Pressure: ambient / Temperature: 300 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||
NMR constraints | NOE 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 representative | Selection criteria: closest to the average | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |