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- PDB-2k7l: NMR structure of a complex formed by the C-terminal domain of hum... -

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Basic information

Entry
Database: PDB / ID: 2k7l
TitleNMR structure of a complex formed by the C-terminal domain of human RAP74 and a phosphorylated peptide from the central domain of the FCP1
Components
  • General transcription factor IIF subunit 1
  • centFCP1-T584PO4 peptide
KeywordsTRANSCRIPTION / TFIIF / FCP1 / phosphorylation / CK2 / RAP74 / Nucleus / Phosphoprotein / Polymorphism / Transcription regulation
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 / exit from mitosis / positive regulation by host of viral transcription / Abortive elongation of HIV-1 transcript in the absence of Tat / 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 / exit from mitosis / positive regulation by host of viral transcription / 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 / myosin phosphatase activity / 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 / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / transcription factor TFIID complex / mRNA Capping / mRNA Splicing - Minor Pathway / 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 / 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 / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / protein dephosphorylation / transcription elongation by RNA polymerase II / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / negative regulation of protein binding / TP53 Regulates Transcription of DNA Repair Genes / 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
Model type detailsminimized average
AuthorsYang, A. / Abbott, K.L. / Desjardins, A. / Di Lello, P. / Omichinski, J.G. / Legault, P.
CitationJournal: Biochemistry / Year: 2009
Title: NMR structure of a complex formed by the carboxyl-terminal domain of human RAP74 and a phosphorylated peptide from the central domain of the FCP1 phosphatase
Authors: Yang, A. / Abbott, K.L. / Desjardins, A. / Di Lello, P. / Omichinski, J.G. / Legault, P.
History
DepositionAug 13, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _pdbx_database_status.status_code_cs / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: centFCP1-T584PO4 peptide
A: General transcription factor IIF subunit 1


Theoretical massNumber of molelcules
Total (without water)10,3052
Polymers10,3052
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 21all calculated structures submitted
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide centFCP1-T584PO4 peptide


Mass: 2398.470 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 451 to 517) / Source method: obtained synthetically
Details: The peptide was chemically synthesized by the solid-phase method
References: UniProt: Q9Y5B0*PLUS
#2: Protein General transcription factor IIF subunit 1 / Transcription initiation factor IIF subunit alpha / TFIIF-alpha / Transcription initiation factor ...Transcription initiation factor IIF subunit alpha / TFIIF-alpha / Transcription initiation factor RAP74 / General transcription factor IIF polypeptide 1 74 kDa subunit protein


Mass: 7906.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2F1, RAP74 / Production host: Escherichia coli (E. coli) / Strain (production host): Topp2 / References: UniProt: P35269

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1332D 1H-13C HSQC
1413D HNHA
1523D HN(CA)CB
1623D HNCO
1723D CBCA(CO)NH
1833D (H)CCH-TOCSY
1933D (H)CCH-COSY
11013D 1H-15N NOESY
11123D CCCTOCSY-NHH
11223D HCCTOCSY-NHH
11333D 13C-edited HMQC-NOESY
1143(HB)CB(CGCD)HD ARO
1153(HB)CB(CGCDCE)HE ARO
11632D isotope filtered 1H-1H TOCSY
11732D isotope filtered 1H-1H NOESY
11822D isotope filtered 1H-1H TOCSY
11922D isotope filtered 1H-1H NOESY
12022D 13C F1-filtered, F2-edited NOESY
12133D 15N/13C F1-filtered, F3-edited NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-98% 15N] cterRAP74, 1 mM centFCP1-T584PO4, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-98% 13C; U-98% 15N] cterRAP74, 1 mM centFCP1-T584PO4, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-98% 13C; U-98% 15N] cterRAP74, 1 mM centFCP1-T584PO4, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMcterRAP74[U-98% 15N]1
1 mMcentFCP1-T584PO41
1 mMcterRAP74[U-98% 13C; U-98% 15N]2
1 mMcentFCP1-T584PO42
1 mMcterRAP74[U-98% 13C; U-98% 15N]3
1 mMcentFCP1-T584PO43
Sample conditionsIonic strength: 10-40 / pH: 6.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.2.2_01Johnson, One Moon Scientificdata analysis
NMRView5.2.2_01Johnson, One Moon Scientificchemical shift assignment
NMRView5.2.2_01Johnson, One Moon Scientificpeak picking
NMRDraw2.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDraw2.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 21 / Conformers submitted total number: 21

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