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- EMDB-17035: Subsection of a helical nucleocapsid of the Respiratory Syncytial... -

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Basic information

Entry
Database: EMDB / ID: EMD-17035
TitleSubsection of a helical nucleocapsid of the Respiratory Syncytial Virus
Map dataSubsection of a helical nucleocapsid of the Respiratory Syncytial Virus.
Sample
  • Organelle or cellular component: RSV recombinant nucleocapsid
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (5'-R(P*CP*CP*CP*CP*CP*CP*C)-3')
KeywordsN-RNA / RSV / nucleoprotein / nucleocapsid / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / helical viral capsid / viral nucleocapsid / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / ribonucleoprotein complex / : / RNA binding
Similarity search - Function
Pneumovirus nucleocapsid protein / Pneumovirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesRespiratory syncytial virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsGonnin L / Desfosses A / Eleouet JF / Galloux M / 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_17035.png

Downloads & links

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Map

FileDownload / File: emd_17035.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubsection of a helical 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: 0.4
Minimum - Maximum-1.2832341 - 1.8835288
Average (Standard dev.)-0.00016830345 (±0.027739635)
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: Subsection of a helical nucleocapsid of the Respiratory...

Fileemd_17035_half_map_1.map
AnnotationSubsection of a helical 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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Half map: Subsection of a helical nucleocapsid of the Respiratory...

Fileemd_17035_half_map_2.map
AnnotationSubsection of a helical 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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Sample components

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Entire : RSV recombinant nucleocapsid

EntireName: RSV recombinant nucleocapsid
Components
  • Organelle or cellular component: RSV recombinant nucleocapsid
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (5'-R(P*CP*CP*CP*CP*CP*CP*C)-3')

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Supramolecule #1: RSV recombinant nucleocapsid

SupramoleculeName: RSV recombinant nucleocapsid / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Respiratory syncytial virus

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Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Respiratory syncytial virus
Molecular weightTheoretical: 41.971152 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: ALSKVKLNDT LNKDQLLSSS KYTIQRSTGD SIDTPNYDVQ KHINKLCGML LITEDANHKF TGLIGMLYAM SRLGREDTIK ILRDAGYHV KANGVDVTTH RQDINGKEMK FEVLTLASLT TEIQINIEIE SRKSYKKMLK EMGEVAPEYR HDSPDCGMII L CIAALVIT ...String:
ALSKVKLNDT LNKDQLLSSS KYTIQRSTGD SIDTPNYDVQ KHINKLCGML LITEDANHKF TGLIGMLYAM SRLGREDTIK ILRDAGYHV KANGVDVTTH RQDINGKEMK FEVLTLASLT TEIQINIEIE SRKSYKKMLK EMGEVAPEYR HDSPDCGMII L CIAALVIT KLAAGDRSGL TAVIRRANNV LKNEMKRYKG LLPKDIANSF YEVFEKHPHF IDVFVHFGIA QSSTRGGSRV EG IFAGLFM NAYGAGQVML RWGVLAKSVK NIMLGHASVQ AEMEQVVEVY EYAQKLGGEA GFYHILNNPK ASLLSLTQFP HFS SVVLGN AAGLGIMGEY RGTPRNQDLY DAAKAYAEQL KENGVINYSV LDLTAEELEA IK

UniProtKB: Nucleoprotein

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Macromolecule #2: RNA (5'-R(P*CP*CP*CP*CP*CP*CP*C)-3')

MacromoleculeName: RNA (5'-R(P*CP*CP*CP*CP*CP*CP*C)-3') / type: rna / ID: 2 / Number of copies: 5
Source (natural)Organism: Respiratory syncytial virus
Molecular weightTheoretical: 2.091315 KDa
SequenceString:
CCCCCCC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 40.0 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: 0.9 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 389540
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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