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- EMDB-17034: Helical nucleocapsid of the N1-370 mutant of the human Respirator... -

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Basic information

Entry
Database: EMDB / ID: EMD-17034
TitleHelical nucleocapsid of the N1-370 mutant of the human Respiratory Syncytial Virus
Map dataHelical nucleocapsid of the N1-370 mutant of the Respiratory Syncytial Virus
Sample
  • Complex: Helical nucleocapsid of the N1-370 mutant of the human Respiratory Syncytial Virus
    • Protein or peptide: Truncated nucleoprotein of the human respiratory syncytial virus A strain Long
KeywordsN-RNA / nucleoprotein / nucleocapsidn RSV / VIRAL PROTEIN
Biological speciesHuman respiratory syncytial virus A strain Long
Methodhelical reconstruction / cryo EM / Resolution: 4.3 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_17034.png

Downloads & links

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Map

FileDownload / File: emd_17034.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical nucleocapsid of the N1-370 mutant 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 400 pix.
= 458. Å		1.15 Å/pix.
x 400 pix.
= 458. Å		1.15 Å/pix.
x 400 pix.
= 458. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.145 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.16731168 - 0.4023381
Average (Standard dev.)0.0028134054 (±0.022155682)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 458.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Helical nucleocapsid of the N1-370 mutant of the...

Fileemd_17034_half_map_1.map
AnnotationHelical nucleocapsid of the N1-370 mutant of the Respiratory Syncytial Virus. Half A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Helical nucleocapsid of the N1-370 mutant of the...

Fileemd_17034_half_map_2.map
AnnotationHelical nucleocapsid of the N1-370 mutant 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 : Helical nucleocapsid of the N1-370 mutant of the human Respirator...

EntireName: Helical nucleocapsid of the N1-370 mutant of the human Respiratory Syncytial Virus
Components
  • Complex: Helical nucleocapsid of the N1-370 mutant of the human Respiratory Syncytial Virus
    • Protein or peptide: Truncated nucleoprotein of the human respiratory syncytial virus A strain Long

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Supramolecule #1: Helical nucleocapsid of the N1-370 mutant of the human Respirator...

SupramoleculeName: Helical nucleocapsid of the N1-370 mutant of the human Respiratory Syncytial Virus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Helical nucleocapsid formed by the C-terminallt truncated nucleoprotein (N1-370) of the human respiratory syncytial virus upon overexpression in insect cells and non specific encapsidation of cellular RNA
Source (natural)Organism: Human respiratory syncytial virus A strain Long

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Macromolecule #1: Truncated nucleoprotein of the human respiratory syncytial virus ...

MacromoleculeName: Truncated nucleoprotein of the human respiratory syncytial virus A strain Long
type: protein_or_peptide / ID: 1
Details: C-terminally truncated mutant of the nucleoprotein N of human RSV (N1-370)
Enantiomer: LEVO
Source (natural)Organism: Human respiratory syncytial virus A strain Long
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MALSKVKLND TLNKDQLLSS SKYTIQRSTG DSIDTPNYDV QKHINKLCGM LLITEDANHK FTGLIGMLYA MSRLGREDTI KILRDAGYHV KANGVDVTTH RQDINGKEMK FEVLTLASLT TEIQINIEIE SRKSYKKMLK EMGEVAPEYR HDSPDCGMII LCIAALVITK ...String:
MALSKVKLND TLNKDQLLSS SKYTIQRSTG DSIDTPNYDV QKHINKLCGM LLITEDANHK FTGLIGMLYA MSRLGREDTI KILRDAGYHV KANGVDVTTH RQDINGKEMK FEVLTLASLT TEIQINIEIE SRKSYKKMLK EMGEVAPEYR HDSPDCGMII LCIAALVITK LAAGDRSGLT AVIRRANNVL KNEMKRYKGL LPKDIANSFY EVFEKHPHFI DVFVHFGIAQ SSTRGGSRVE GIFAGLFMNA YGAGQVMLRW GVLAKSVKNI MLGHASVQAE MEQVVEVYEY AQKLGGEAGF YHILNNPKAS LLSLTQFPHF SSVVLGNAAG LGIMGEYRGT PRNQDLYDAA KAYAEQLKEN GVINYSVLDL

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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: 6.58 Å
Applied symmetry - Helical parameters - Δ&Phi: -36 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 329706
Startup modelType of model: NONE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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