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- PDB-6yjl: Solution NMR structure of the C-terminal arm of RSV nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 6yjl
TitleSolution NMR structure of the C-terminal arm of RSV nucleoprotein
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / STRUCTURE FROM CYANA Nuclear Magnetic Resonance Respiratory Syncytial Virus Nucleoprotein Nucleocapsid RNA dependent RNA polymerase Peptide Intrinsically disordered region
Function / homology
Function and homology information


Respiratory syncytial virus genome transcription / symbiont-mediated suppression of host PKR/eIFalpha signaling / Translation of respiratory syncytial virus mRNAs / protein serine/threonine kinase inhibitor activity / Respiratory syncytial virus genome replication / helical viral capsid / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry ...Respiratory syncytial virus genome transcription / symbiont-mediated suppression of host PKR/eIFalpha signaling / Translation of respiratory syncytial virus mRNAs / protein serine/threonine kinase inhibitor activity / Respiratory syncytial virus genome replication / helical viral capsid / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / PKR-mediated signaling / Evasion by RSV of host interferon responses / viral capsid / viral nucleocapsid / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / virus-mediated perturbation of host defense response / RNA binding
Similarity search - Function
Pneumovirus nucleocapsid protein / Pneumovirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesHuman respiratory syncytial virus A
MethodSOLUTION NMR / torsion angle dynamics
AuthorsCardone, C. / Eleouet, J.-F. / Galloux, M. / Sizun, C.
CitationJournal: To Be Published
Title: Solution NMR structure of the C-terminal arm of RSV nucleoprotein
Authors: Cardone, C. / Eleouet, J.-F. / Galloux, M. / Sizun, C.
History
DepositionApr 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2Jun 19, 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: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)3,6281
Polymers3,6281
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4040 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1target function

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Components

#1: Protein/peptide Nucleoprotein / Protein N / Nucleocapsid protein


Mass: 3627.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 361-391
Source: (gene. exp.) Human respiratory syncytial virus A (strain A2)
Strain: A2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03418

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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 HNCO
131isotropic13D HNCA
141isotropic13D HN(CO)CA
151isotropic13D HN(COCA)CB
181isotropic13D HN(CA)CB
171isotropic13D HBHA(CO)NH
161isotropic13D HBHANH
1111isotropic13D H(CCO)NH
1101isotropic12D 1H-13C HSQC
191isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 20 mM unlabeled sodium phosphate, 100 mM unlabeled sodium chloride, 1 mM unlabeled TCEP, 1 mM [U-13C; U-15N] RSV_N_Carm, 93% H2O/7% D2O
Label: 15N13C_sample / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphateunlabeled1
100 mMsodium chlorideunlabeled1
1 mMTCEPunlabeled1
1 mMRSV_N_Carm[U-13C; U-15N]1
Sample conditionsIonic strength: 133 mM / Ionic strength err: 15 / Label: conditions_1 / pH: 6.5 / PH err: 0.2 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 1

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin4Bruker Biospinprocessing
CcpNmr Analysis2.4CCPNchemical shift assignment
CcpNmr Analysis2.4CCPNpeak picking
TALOS4.21Cornilescu, Delaglio and Baxstructure calculation
CYANA3.98Guntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 5
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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