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- PDB-1nha: Solution Structure of the Carboxyl-Terminal Domain of RAP74 and N... -

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Basic information

Entry
Database: PDB / ID: 1nha
TitleSolution Structure of the Carboxyl-Terminal Domain of RAP74 and NMR Characterization of the FCP-Binding Sites of RAP74 and CTD of RAP74, the subunit of Human TFIIF
ComponentsTranscription initiation factor IIF, alpha subunit
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR / HUMAN GENERAL TRANSCRIPTION FACTOR TFIIF / RAP74
Function / homology
Function and homology information


phosphatase activator activity / TFIIF-class transcription factor complex binding / transcription factor TFIIF complex / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / RNA polymerase II general transcription initiation factor binding / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE ...phosphatase activator activity / TFIIF-class transcription factor complex binding / transcription factor TFIIF complex / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / RNA polymerase II general transcription initiation factor binding / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / 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 / Processing of Capped Intron-Containing Pre-mRNA / 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 / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / negative regulation of protein binding / promoter-specific chromatin binding / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / response to virus / cell junction / protein phosphatase binding / Estrogen-dependent gene expression / transcription by RNA polymerase II / protein domain specific binding / intracellular membrane-bounded organelle / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNguyen, B.D. / Chen, H.T. / Kobor, M.S. / Greenblatt, J. / Legault, P. / Omichinski, J.G.
CitationJournal: Biochemistry / Year: 2003
Title: Solution Structure of the Carboxyl-Terminal Domain of RAP74 and NMR Characterization of the FCP1-Binding Sites of RAP74 and Human TFIIB.
Authors: Nguyen, B.D. / Chen, H.T. / Kobor, M.S. / Greenblatt, J. / Legault, P. / Omichinski, J.G.
History
DepositionDec 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription initiation factor IIF, alpha subunit


Theoretical massNumber of molelcules
Total (without water)9,3451
Polymers9,3451
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 67structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

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


Mass: 9344.814 Da / Num. of mol.: 1 / Fragment: C-Terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAP74 / 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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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
1333D 15N/13C-separated NOESY
1443D 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 unlabeled, 20mM sodium phosphate, and 1mM EDTA100% D2O
21mM cterRAP74 U-15N, 20mM sodium phosphate, and 1mM EDTA90% H2O/10% D2O
31mM cterRAP74 U-15N and U-13C, 20mM sodium phosphate, and 1mM EDTA90% H2O/10% D2O
41mM cterRAP74 U-15N and U-13C, 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
NMRPipenullBaxprocessing
PIPPnullGarrettdata analysis
CNSmodified CNS with conformational database potentialKay and Choy, Cloresrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structures are based on a total of 1063 restraints, 959 are NOE-derived distance constraints, 104 dihedral angle restraints
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 67 / Conformers submitted total number: 20

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