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- EMDB-17031: Double-ring nucleocapsid of the Respiratory Syncytial Virus -

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Basic information

Entry
Database: EMDB / ID: EMD-17031
TitleDouble-ring nucleocapsid of the Respiratory Syncytial Virus
Map dataDouble-ring nucleocapsid of the Respiratory Syncytial Virus
Sample
  • Complex: Double ring nucleocapsid of the human Respiratory Syncytial Virus
    • Protein or peptide: Nucleoprotein
  • RNA: RNA (70-mer)
KeywordsD10-symmetry / N-RNA / nucleoprotein / RSV / VIRAL PROTEIN
Function / homology
Function and homology information


Respiratory syncytial virus genome transcription / Translation of respiratory syncytial virus mRNAs / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / Respiratory syncytial virus genome replication / helical viral capsid / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Respiratory syncytial virus (RSV) attachment and entry ...Respiratory syncytial virus genome transcription / Translation of respiratory syncytial virus mRNAs / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / Respiratory syncytial virus genome replication / helical viral capsid / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / 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 / symbiont-mediated suppression of host NF-kappaB cascade / 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 strain Long / Respiratory syncytial virus / Trichoplusia ni (cabbage looper)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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_17031.png

Downloads & links

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Map

FileDownload / File: emd_17031.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDouble-ring nucleocapsid of the Respiratory Syncytial Virus
Projections & slices

Image control

Size
Brightness
Contrast
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: 0.7
Minimum - Maximum-1.8831028 - 3.2154434
Average (Standard dev.)0.0017599929 (±0.058301296)
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: Double-ring nucleocapsid of the Respiratory Syncytial Virus

Fileemd_17031_half_map_1.map
AnnotationDouble-ring nucleocapsid of the Respiratory Syncytial Virus
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Double-ring nucleocapsid of the Respiratory Syncytial Virus

Fileemd_17031_half_map_2.map
AnnotationDouble-ring nucleocapsid of the Respiratory Syncytial Virus
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Double ring nucleocapsid of the human Respiratory Syncytial Virus

EntireName: Double ring nucleocapsid of the human Respiratory Syncytial Virus
Components
  • Complex: Double ring nucleocapsid of the human Respiratory Syncytial Virus
    • Protein or peptide: Nucleoprotein
  • RNA: RNA (70-mer)

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Supramolecule #1: Double ring nucleocapsid of the human Respiratory Syncytial Virus

SupramoleculeName: Double ring nucleocapsid of the human Respiratory Syncytial Virus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Double ring nucleocapsid 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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Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Respiratory syncytial virus
Molecular weightTheoretical: 43.507848 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MALSKVKLND TLNKDQLLSS SKYTIQRSTG DSIDTPNYDV QKHINKLCGM LLITEDANHK FTGLIGMLYA MSRLGREDTI KILRDAGYH VKANGVDVTT HRQDINGKEM KFEVLTLASL TTEIQINIEI ESRKSYKKML KEMGEVAPEY RHDSPDCGMI I LCIAALVI ...String:
MALSKVKLND TLNKDQLLSS SKYTIQRSTG DSIDTPNYDV QKHINKLCGM LLITEDANHK FTGLIGMLYA MSRLGREDTI KILRDAGYH VKANGVDVTT HRQDINGKEM KFEVLTLASL TTEIQINIEI ESRKSYKKML KEMGEVAPEY RHDSPDCGMI I LCIAALVI TKLAAGDRSG LTAVIRRANN VLKNEMKRYK GLLPKDIANS FYEVFEKHPH FIDVFVHFGI AQSSTRGGSR VE GIFAGLF MNAYGAGQVM LRWGVLAKSV KNIMLGHASV QAEMEQVVEV YEYAQKLGGE AGFYHILNNP KASLLSLTQF PHF SSVVLG NAAGLGIMGE YRGTPRNQDL YDAAKAYAEQ LKENGVINYS VLDLTAEELE AIKHQLNPKD NDVEL

UniProtKB: Nucleoprotein

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Macromolecule #2: RNA (70-mer)

MacromoleculeName: RNA (70-mer) / type: rna / ID: 2 / Number of copies: 2
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 21.317777 KDa
SequenceString:
CCCCCCCCCC CCCCCCCCCC CCCCCCCCCC CCCCCCCCCC CCCCCCCCCC CCCCCCCCCC CCCCCCCCCC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle 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

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D10 (2x10 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47212
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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