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- EMDB-17030: Helical nucleocapsid of the Respiratory Syncytial Virus -

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Basic information

Entry
Database: EMDB / ID: EMD-17030
TitleHelical nucleocapsid of the Respiratory Syncytial Virus
Map dataHelical nucleocapsid of the Respiratory Syncytial Virus
Sample
  • Complex: Helical nucleocapsid of the human Respiratory Syncytial Virus
KeywordsHelical symmetry / N-RNA / nucleocapsid / RSV / VIRAL PROTEIN
Biological speciesHuman respiratory syncytial virus A strain Long
Methodhelical reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsGonnin L / Desfosses A / Gutsche I
Funding support France, 1 items
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, 2023-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateSep 27, 2023-
Current statusSep 27, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17030.png

Downloads & links

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Map

FileDownload / File: emd_17030.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical nucleocapsid of the Respiratory Syncytial Virus
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 440 pix.
= 503.8 Å		1.15 Å/pix.
x 440 pix.
= 503.8 Å		1.15 Å/pix.
x 440 pix.
= 503.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.145 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.2569721 - 0.63136417
Average (Standard dev.)0.0035037156 (±0.025450427)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 503.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Helical nucleocapsid of the Respiratory Syncytial Virus. Half B

Fileemd_17030_half_map_1.map
AnnotationHelical nucleocapsid of the Respiratory Syncytial Virus. Half B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Helical nucleocapsid of the Respiratory Syncytial Virus. Half A

Fileemd_17030_half_map_2.map
AnnotationHelical nucleocapsid of the Respiratory Syncytial Virus. Half A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Helical nucleocapsid of the human Respiratory Syncytial Virus

EntireName: Helical nucleocapsid of the human Respiratory Syncytial Virus
Components
  • Complex: Helical nucleocapsid of the human Respiratory Syncytial Virus

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Supramolecule #1: Helical nucleocapsid of the human Respiratory Syncytial Virus

SupramoleculeName: Helical nucleocapsid of the human Respiratory Syncytial Virus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Helical nucleocapsid with a non-canonical symmetry formed by the nucleoprotein N of the human RSV upon overexpression in insect cells and encapsidation of cellular RNA
Source (natural)Organism: Human respiratory syncytial virus A strain Long

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 105.3 Å
Applied symmetry - Helical parameters - Δ&Phi: 149.453 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 389540
Startup modelType of model: NONE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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