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- PDB-2n0y: NMR structure of the complex between the C-terminal domain of the... -

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Basic information

Entry
Database: PDB / ID: 2n0y
TitleNMR structure of the complex between the C-terminal domain of the Rift Valley fever virus protein NSs and the PH domain of the Tfb1 subunit of TFIIH
Components
  • Non-structural protein NS-S
  • RNA polymerase II transcription factor B subunit 1
KeywordsTRANSCRIPTION/VIRAL PROTEIN / transcription / virulence / viral protein-transcription complex / drug target / virus-host interface / TRANSCRIPTION-VIRAL PROTEIN complex
Function / homology
Function and homology information


symbiont-mediated suppression of host transcription initiation from RNA polymerase II promoter / symbiont-mediated suppression of host transcription / suppression by virus of host type I interferon production / symbiont-mediated suppression of host PKR/eIFalpha signaling / phosphatidylinositol-5-phosphate binding / nucleotide-excision repair factor 3 complex / phosphatidylinositol-3-phosphate binding / negative stranded viral RNA replication / protein serine/threonine kinase inhibitor activity / transcription factor TFIIH core complex ...symbiont-mediated suppression of host transcription initiation from RNA polymerase II promoter / symbiont-mediated suppression of host transcription / suppression by virus of host type I interferon production / symbiont-mediated suppression of host PKR/eIFalpha signaling / phosphatidylinositol-5-phosphate binding / nucleotide-excision repair factor 3 complex / phosphatidylinositol-3-phosphate binding / negative stranded viral RNA replication / protein serine/threonine kinase inhibitor activity / 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 / symbiont-mediated suppression of host gene expression / host cell cytoplasm / transcription by RNA polymerase II / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / DNA repair / host cell nucleus / nucleus / cytosol
Similarity search - Function
Phlebovirus, non structural protein / Rift valley fever virus non structural protein-like / Rift valley fever virus non structural protein (NSs) like / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. ...Phlebovirus, non structural protein / Rift valley fever virus non structural protein-like / Rift valley fever virus non structural protein (NSs) like / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Non-structural protein S / General transcription and DNA repair factor IIH subunit TFB1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Rift valley fever virus
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsCyr, N. / de la Fuente, C. / Lecoq, L. / Guendel, I. / Chabot, P.R. / Kehn-Hall, K. / Omichinski, J.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: A Omega XaV motif in the Rift Valley fever virus NSs protein is essential for degrading p62, forming nuclear filaments and virulence.
Authors: Cyr, N. / de la Fuente, C. / Lecoq, L. / Guendel, I. / Chabot, P.R. / Kehn-Hall, K. / Omichinski, J.G.
History
DepositionMar 18, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2May 20, 2015Group: Database references
Revision 1.3May 27, 2015Group: Database references
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase II transcription factor B subunit 1
B: Non-structural protein NS-S


Theoretical massNumber of molelcules
Total (without water)15,4702
Polymers15,4702
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-1.8 kcal/mol
Surface area8620 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 260structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA polymerase II transcription factor B subunit 1 / General transcription and DNA repair factor IIH subunit TFB1 / TFIIH subunit TFB1 / RNA polymerase ...General transcription and DNA repair factor IIH subunit TFB1 / TFIIH subunit TFB1 / RNA polymerase II transcription factor B 73 kDa subunit / RNA polymerase II transcription factor B p73 subunit


Mass: 12903.701 Da / Num. of mol.: 1 / Fragment: Pleckstrin homology domain residues 1-115 / Mutation: M1P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: D9740.3, TFB1, YDR311W / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 / References: UniProt: P32776
#2: Protein/peptide Non-structural protein NS-S


Mass: 2566.487 Da / Num. of mol.: 1 / Fragment: C-terminal domain residues247-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rift valley fever virus / Strain: ZH-548 M12 / Gene: NSS / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 / References: UniProt: P21698

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1262D 1H-15N HSQC
1313D (H)CCH-TOCSY
1443D (H)CCH-TOCSY
1513D HNCO
1643D HNCO
1713D HN(CA)CB
1843D HN(CA)CB
1922D 1H-13C HSQC
11052D 1H-13C HSQC
11123D 1H-13C NOESY
11253D 1H-13C NOESY
11323D 1H-13C NOESY aromatic
11453D 1H-13C NOESY aromatic
11522D 1H-13C HSQC aromatic
11652D 1H-13C HSQC aromatic
11723D 1H-13C NOESY intermolecular
11853D 1H-13C NOESY intermolecular

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C; U-15N] RNA polymerase II transcription factor B subunit 1, 2 mM Non-structural protein NS-S, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N] RNA polymerase II transcription factor B subunit 1, 2 mM Non-structural protein NS-S, 100% D2O100% D2O
30.5 mM [U-15N] RNA polymerase II transcription factor B subunit 1, 1 mM Non-structural protein NS-S, 90% H2O/10% D2O90% H2O/10% D2O
41 mM RNA polymerase II transcription factor B subunit 1, 0.5 mM [U-13C; U-15N] Non-structural protein NS-S, 90% H2O/10% D2O90% H2O/10% D2O
50.5 mM RNA polymerase II transcription factor B subunit 1, 1 mM [U-13C; U-15N] Non-structural protein NS-S, 100% D2O100% D2O
60.4 mM RNA polymerase II transcription factor B subunit 1, 0.2 mM [U-15N] Non-structural protein NS-S, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRNA polymerase II transcription factor B subunit 1-1[U-13C; U-15N]1
2 mMNon-structural protein NS-S-21
1 mMRNA polymerase II transcription factor B subunit 1-3[U-13C; U-15N]2
2 mMNon-structural protein NS-S-42
0.5 mMRNA polymerase II transcription factor B subunit 1-5[U-15N]3
1 mMNon-structural protein NS-S-63
1 mMRNA polymerase II transcription factor B subunit 1-74
0.5 mMNon-structural protein NS-S-8[U-13C; U-15N]4
0.5 mMRNA polymerase II transcription factor B subunit 1-95
1 mMNon-structural protein NS-S-10[U-13C; U-15N]5
0.4 mMRNA polymerase II transcription factor B subunit 1-116
0.2 mMNon-structural protein NS-S-12[U-15N]6
Sample conditionsIonic strength: 0 / pH: 6.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionClassification
CcpNmr Analysis2.3.1data analysis
CNSrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 3053 / NOE intraresidue total count: 1190 / NOE long range total count: 794 / NOE medium range total count: 417 / NOE sequential total count: 622 / Protein phi angle constraints total count: 111 / Protein psi angle constraints total count: 111
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 260 / Conformers submitted total number: 20

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