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- PDB-6yp5: Solution NMR structure of the oligomerization domain of respirato... -

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Basic information

Entry
Database: PDB / ID: 6yp5
TitleSolution NMR structure of the oligomerization domain of respiratory syncytial virus phosphoprotein
ComponentsPhosphoprotein
KeywordsVIRAL PROTEIN / Phosphoprotein / RNA dependent RNA polymerase cofactor / Tetramer / Coiled-coil
Function / homologyPhosphoprotein, pneumoviral / Pneumovirus phosphoprotein / virion component => GO:0044423 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / host cell cytoplasm / RNA-dependent RNA polymerase activity / cytoplasm / Phosphoprotein
Function and homology information
Biological speciesRespiratory syncytial virus
MethodSOLUTION NMR / simulated annealing
AuthorsCardone, C. / Bontems, F. / Bardiaux, B. / Sizun, C.
CitationJournal: Biomolecules / Year: 2021
Title: A Structural and Dynamic Analysis of the Partially Disordered Polymerase-Binding Domain in RSV Phosphoprotein.
Authors: Cardone, C. / Caseau, C.M. / Bardiaux, B. / Thureaux, A. / Galloux, M. / Bajorek, M. / Eleouet, J.F. / Litaudon, M. / Bontems, F. / Sizun, C.
History
DepositionApr 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 24, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoprotein
B: Phosphoprotein
C: Phosphoprotein
D: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)18,2444
Polymers18,2444
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area6220 Å2
ΔGint-56 kcal/mol
Surface area8410 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide
Phosphoprotein /


Mass: 4561.035 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-terminal residues GLY119 to SER126 are leftovers from the expression tag. Residues GLY119 to SER124 were not included in the structure calculation.
Source: (gene. exp.) Respiratory syncytial virus / Plasmid: pGEX-P(127-163) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8FRA5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCA
131isotropic13D HN(CO)CA
141isotropic13D HN(CA)CB
151isotropic13D HNCO
1131isotropic13D HN(COCA)CB
1121isotropic13D HBHA(CO)NH
1111isotropic13D CBCA(CO)NH
1102isotropic23D (H)CCH-TOCSY
192isotropic22D 1H-15N HSQC
182isotropic22D 1H-13C HSQC
171isotropic32D 1H-15N HSQC
161isotropic32D 1H-13C HSQC
1171isotropic33D 1H-15N NOESY-HSQC
1162isotropic31D 1H
1152isotropic32D 1H-13C HSQC
1142isotropic33D 1H-13C NOESY
1203isotropic32D 1H-13C HSQC
1193isotropic31H-13C NOESY-HSQC with 13C/15N filter in F1

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1600 uM [U-13C; U-15N] Phosphoprotein(127-163), 20 mM sodium phosphate, 100 mM sodium chloride, 93% H2O/7% D2O15N13C_POD_H2O93% H2O/7% D2O
solution2600 uM [U-13C; U-15N] Phosphoprotein(127-163), 20 mM sodium phosphate, 100 mM sodium chloride, 100% D2O15N13C_POD_D2O100% D2O
solution3300 uM [U-13C; U-15N] Phosphoprotein(127-163), 300 uM Phosphoprotein(127-163), 20 mM sodium phosphate, 100 mM sodium chloride, 100% D2O15N13C_14N12C_POD_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uMPhosphoprotein(127-163) [U-13C; U-15N][U-13C; U-15N]1
20 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
600 uMPhosphoprotein(127-163) [U-13C; U-15N][U-13C; U-15N]2
20 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
300 uMPhosphoprotein(127-163) [U-13C; U-15N][U-13C; U-15N]3
300 uMPhosphoprotein(127-163)natural abundance3
20 mMsodium phosphatenatural abundance3
100 mMsodium chloridenatural abundance3
Sample conditionsIonic strength: 133 mM / Ionic strength err: 20 / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002
Bruker AVANCE IIIBrukerAVANCE III9503

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
CcpNmr Analysis2.4CCPNchemical shift assignment
CcpNmr Analysis2.4CCPNpeak picking
TALOS-N4.21Shen and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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