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- PDB-8op1: Subsection of a helical nucleocapsid of the Respiratory Syncytial... -

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Basic information

Entry
Database: PDB / ID: 8op1
TitleSubsection of a helical nucleocapsid of the Respiratory Syncytial Virus
Components
  • Nucleoprotein
  • RNA (5'-R(P*CP*CP*CP*CP*CP*CP*C)-3')
KeywordsVIRAL PROTEIN / N-RNA / RSV / nucleoprotein / nucleocapsid
Function / homology
Function and homology information


symbiont-mediated suppression of host PKR/eIFalpha signaling / helical viral capsid / protein serine/threonine kinase inhibitor activity / viral nucleocapsid / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / RNA binding
Similarity search - Function
Pneumovirus nucleocapsid protein / Pneumovirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesRespiratory syncytial virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsGonnin, L. / Desfosses, A. / Eleouet, J.F. / Galloux, M. / Gutsche, I.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR DecRisp ANR-19-CE11-0017-01 France
CitationJournal: Nat Commun / Year: 2023
Title: Structural landscape of the respiratory syncytial virus nucleocapsids.
Authors: Lorène Gonnin / Ambroise Desfosses / Maria Bacia-Verloop / Didier Chevret / Marie Galloux / Jean-François Éléouët / Irina Gutsche /
Abstract: Human Respiratory Syncytial Virus (HRSV) is a prevalent cause of severe respiratory infections in children and the elderly. The helical HRSV nucleocapsid is a template for the viral RNA synthesis and ...Human Respiratory Syncytial Virus (HRSV) is a prevalent cause of severe respiratory infections in children and the elderly. The helical HRSV nucleocapsid is a template for the viral RNA synthesis and a scaffold for the virion assembly. This cryo-electron microscopy analysis reveals the non-canonical arrangement of the HRSV nucleocapsid helix, composed of 16 nucleoproteins per asymmetric unit, and the resulting systematic variations in the RNA accessibility. We demonstrate that this unique helical symmetry originates from longitudinal interactions by the C-terminal arm of the HRSV nucleoprotein. We explore the polymorphism of the nucleocapsid-like assemblies, report five structures of the full-length particles and two alternative arrangements formed by a C-terminally truncated nucleoprotein mutant, and demonstrate the functional importance of the identified longitudinal interfaces. We put all these findings in the context of the HRSV RNA synthesis machinery and delineate the structural basis for its further investigation.
History
DepositionApr 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.0Sep 27, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 27, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 27, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 27, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 27, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
F: RNA (5'-R(P*CP*CP*CP*CP*CP*CP*C)-3')
B: Nucleoprotein
G: RNA (5'-R(P*CP*CP*CP*CP*CP*CP*C)-3')
C: Nucleoprotein
H: RNA (5'-R(P*CP*CP*CP*CP*CP*CP*C)-3')
D: Nucleoprotein
I: RNA (5'-R(P*CP*CP*CP*CP*CP*CP*C)-3')
E: Nucleoprotein
J: RNA (5'-R(P*CP*CP*CP*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)220,31210
Polymers220,31210
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Nucleoprotein


Mass: 41971.152 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Respiratory syncytial virus / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C3UPA9
#2: RNA chain
RNA (5'-R(P*CP*CP*CP*CP*CP*CP*C)-3')


Mass: 2091.315 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Respiratory syncytial virus / Production host: Trichoplusia ni (cabbage looper)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RSV recombinant nucleocapsid / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Respiratory syncytial virus
Source (recombinant)Organism: Trichoplusia ni (cabbage looper) / Strain: High Five
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 389540 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00615720
ELECTRON MICROSCOPYf_angle_d0.69521315
ELECTRON MICROSCOPYf_dihedral_angle_d6.232450
ELECTRON MICROSCOPYf_chiral_restr0.0462450
ELECTRON MICROSCOPYf_plane_restr0.0042620

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