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Yorodumi- PDB-1onv: NMR Structure of a Complex Containing the TFIIF Subunit RAP74 and... -
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-Basic information
Entry | Database: PDB / ID: 1onv | ||||||
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Title | NMR Structure of a Complex Containing the TFIIF Subunit RAP74 and the RNAP II CTD Phosphatase FCP1 | ||||||
Components |
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Keywords | TRANSCRIPTION / Transcription Factor / Human General Transcription Factor TFIIF / RAP74 / RNA Polymerase II CTD Phosphatase / TFIIF-associating CTD Phosphatase / FCP1 | ||||||
Function / homology | Function and homology information RNA polymerase II CTD heptapeptide repeat phosphatase activity / negative regulation of cell growth involved in cardiac muscle cell development / Tat protein binding / phosphatase activator activity / TFIIF-class transcription factor complex binding / transcription factor TFIIF complex / positive regulation by host of viral transcription / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA polymerase II general transcription initiation factor binding / FGFR2 alternative splicing ...RNA polymerase II CTD heptapeptide repeat phosphatase activity / negative regulation of cell growth involved in cardiac muscle cell development / Tat protein binding / phosphatase activator activity / TFIIF-class transcription factor complex binding / transcription factor TFIIF complex / positive regulation by host of viral transcription / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA polymerase II general transcription initiation factor binding / FGFR2 alternative splicing / exit from mitosis / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / myosin phosphatase activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / RNA polymerase II general transcription initiation factor activity / mRNA Capping / protein-serine/threonine phosphatase / 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 / mRNA Splicing - Minor Pathway / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / phosphoprotein phosphatase activity / Processing of Capped Intron-Containing Pre-mRNA / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / spindle midzone / Formation of HIV elongation complex in the absence of HIV Tat / positive regulation of transcription elongation by RNA polymerase II / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / protein dephosphorylation / mRNA Splicing - Major Pathway / negative regulation of protein binding / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / transcription elongation by RNA polymerase II / response to virus / spindle pole / spindle / cell junction / midbody / protein phosphatase binding / Estrogen-dependent gene expression / transcription by RNA polymerase II / protein domain specific binding / cell division / intracellular membrane-bounded organelle / centrosome / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Nguyen, B.D. / Abbott, K.L. / Potempa, K. / Kobor, M.S. / Archambault, J. / Greenblatt, J. / Legault, P. / Omichinski, J.G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: NMR Structure of a Complex Containing the TFIIF Subunit RAP74 and the RNA polymerase II carboxyl-terminal domain phosphatase FCP1 Authors: Nguyen, B.D. / Abbott, K.L. / Potempa, K. / Kobor, M.S. / Archambault, J. / Greenblatt, J. / Legault, P. / Omichinski, J.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 1onv.cif.gz | 565.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1onv.ent.gz | 467 KB | Display | PDB format |
PDBx/mmJSON format | 1onv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1onv_validation.pdf.gz | 362.1 KB | Display | wwPDB validaton report |
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Full document | 1onv_full_validation.pdf.gz | 638.8 KB | Display | |
Data in XML | 1onv_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 1onv_validation.cif.gz | 51.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/1onv ftp://data.pdbj.org/pub/pdb/validation_reports/on/1onv | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 9344.814 Da / Num. of mol.: 1 Fragment: C-Terminal Domain of RAP74, sequence database residues 436-517 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: GST-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35269 |
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#2: Protein | Mass: 9022.545 Da / Num. of mol.: 1 Fragment: C-Terminal Domain of FCP1, sequence database residues 760-842 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: GST-3X / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5B0 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 20mM sodium phosphate buffer / pH: 6.5 / Pressure: ambient / Temperature: 300 K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | ||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 Details: The structures were determined based on a total of 1267 restraints, 1131 NOE-derived distance restraints (including 58 intermolecular NOE-derived distance restraints) and 136 dihedral angle restraints | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average,minimized average structure | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 70 / Conformers submitted total number: 20 |