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- PDB-1onv: NMR Structure of a Complex Containing the TFIIF Subunit RAP74 and... -

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Basic information

Entry
Database: PDB / ID: 1onv
TitleNMR Structure of a Complex Containing the TFIIF Subunit RAP74 and the RNAP II CTD Phosphatase FCP1
Components
  • Transcription initiation factor IIF, alpha subunit
  • serine phosphatase FCP1a
KeywordsTRANSCRIPTION / 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 / phosphatase activator activity / TFIIF-class transcription factor complex binding / transcription factor TFIIF complex / exit from mitosis / Tat protein binding / host-mediated activation of viral transcription / RNA polymerase II general transcription initiation factor binding / Abortive elongation of HIV-1 transcript in the absence of Tat ...RNA polymerase II CTD heptapeptide repeat phosphatase activity / negative regulation of cell growth involved in cardiac muscle cell development / phosphatase activator activity / TFIIF-class transcription factor complex binding / transcription factor TFIIF complex / exit from mitosis / Tat protein binding / host-mediated activation of viral transcription / RNA polymerase II general transcription initiation factor binding / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / protein-serine/threonine phosphatase / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / spindle midzone / 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 / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / phosphoprotein phosphatase activity / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / protein dephosphorylation / negative regulation of protein binding / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / promoter-specific chromatin binding / positive regulation of transcription elongation by RNA polymerase II / response to virus / spindle / spindle pole / 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
FCP1-like phosphatase, C-terminal / FCP1, C-terminal / FCP1-like phosphatase, phosphatase domain / CTD phosphatase Fcp1 / FCP1 homology domain / NLI interacting factor-like phosphatase / FCP1 homology domain profile. / catalytic domain of ctd-like phosphatases / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) ...FCP1-like phosphatase, C-terminal / FCP1, C-terminal / FCP1-like phosphatase, phosphatase domain / CTD phosphatase Fcp1 / FCP1 homology domain / NLI interacting factor-like phosphatase / FCP1 homology domain profile. / catalytic domain of ctd-like phosphatases / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / HAD superfamily / HAD-like superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
General transcription factor IIF subunit 1 / RNA polymerase II subunit A C-terminal domain phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNguyen, B.D. / Abbott, K.L. / Potempa, K. / Kobor, M.S. / Archambault, J. / Greenblatt, J. / Legault, P. / Omichinski, J.G.
CitationJournal: 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
DepositionMar 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: Transcription initiation factor IIF, alpha subunit
B: serine phosphatase FCP1a


Theoretical massNumber of molelcules
Total (without water)18,3672
Polymers18,3672
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 / 70structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average,minimized average structure

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Components

#1: Protein Transcription initiation factor IIF, alpha subunit / TFIIF-alfa / Transcription initiation factor RAP74


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
#2: Protein serine phosphatase FCP1a


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
133HNCO, (HB)CBCA(CO)NNH, HN(CA)CB, H(CCO)NNH-TOCSY, C(CO)NNH-TOCSY
1443D 15N-separated NOESY
155HNCO, (HB)CBCA(CO)NNH, HN(CA)CB, H(CCO)NNH-TOCSY, C(CO)NNH-TOCSY
1663D 13C-separated NOESY
1762D 13C-filterd/edited NOESY
1873D 13C-filterd/edited NOESY
1953D 15N/13C separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM cterRAP74/cterFCP1, 20mM sodium phosphate, and 1mM EDTA100% D2O
21mM U-15N cterRAP74/cterFCP1, 20mM sodium phosphate, and 1mM EDTA90% H2O/10% D2O
31mM U-15N,13C cterRAP74/cterFCP1, 20mM sodium phosphate, and 1mM EDTA90% H2O/10% D2O
41mM cterRAP74/U-15N cterFCP1, 20mM sodium phosphate, and 1mM EDTA90% H2O/10% D2O
51mM cterRAP74/U-15N,13C cterFCP1, 20mM sodium phosphate, and 1mM EDTA90% H2O/10% D2O
61mM U-15N,C13 cterRAP74/cterFCP1, 20mM sodium phosphate, and 1mM EDTA;100% D2O
71mM cterRAP74/U-15N,13C cterFCP1, 20mM sodium phosphate, and 1mM EDTA100% D2O
Sample conditionsIonic strength: 20mM sodium phosphate buffer / pH: 6.5 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1Brungerstructure solution
NMRPipeBaxprocessing
PIPPGarrettdata analysis
NMRView5Johnsondata analysis
CNSmodified CNS with conformational database potentialKay and Choy, Cloresrefinement
RefinementMethod: 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 representativeSelection criteria: closest to the average,minimized average structure
NMR ensembleConformer 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

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