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- EMDB-35728: respiratory syncytial virus nucleocapsid-like assembly -

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Basic information

Entry
Database: EMDB / ID: EMD-35728
Titlerespiratory syncytial virus nucleocapsid-like assembly
Map data
Sample
  • Complex: respiratory syncytial virus nucleocapsid-like assembly
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (35-MER)
Keywordsrespiratory syncytial virus / nucleocapsid-like assembly / Cryo-EM / 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 / ribonucleoprotein complex / RNA binding
Similarity search - Function
Pneumovirus nucleocapsid protein / Pneumovirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesHuman respiratory syncytial virus A / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.96 Å
AuthorsWang Y / Luo Y / Ling X / Luo B / Jia G / Dong H / Su Z
Funding support China, 4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303700 China
Ministry of Science and Technology (MoST, China)2021YFA1301900 China
National Natural Science Foundation of China (NSFC)32222040 China
National Natural Science Foundation of China (NSFC)32070049 China
CitationJournal: Signal Transduct Target Ther / Year: 2023
Title: Cryo-EM structure of the nucleocapsid-like assembly of respiratory syncytial virus.
Authors: Yan Wang / Chong Zhang / Yongbo Luo / Xiaobin Ling / Bingnan Luo / Guowen Jia / Dan Su / Haohao Dong / Zhaoming Su /
Abstract: Respiratory syncytial virus (RSV) is a nonsegmented, negative strand RNA virus that has caused severe lower respiratory tract infections of high mortality rates in infants and the elderly, yet no ...Respiratory syncytial virus (RSV) is a nonsegmented, negative strand RNA virus that has caused severe lower respiratory tract infections of high mortality rates in infants and the elderly, yet no effective vaccine or antiviral therapy is available. The RSV genome encodes the nucleoprotein (N) that forms helical assembly to encapsulate and protect the RNA genome from degradation, and to serve as a template for transcription and replication. Previous crystal structure revealed a decameric ring architecture of N in complex with the cellular RNA (N-RNA) of 70 nucleotides (70-nt), whereas cryo-ET reconstruction revealed a low-resolution left-handed filament, in which the crystal monomer structure was docked with the helical symmetry applied to simulate a nucleocapsid-like assembly of RSV. However, the molecular details of RSV nucleocapsid assembly remain unknown, which continue to limit our complete understanding of the critical interactions involved in the nucleocapsid and antiviral development that may target this essential process during the viral life cycle. Here we resolve the near-atomic cryo-EM structure of RSV N-RNA that represents roughly one turn of the helical assembly that unveils critical interaction interfaces of RSV nucleocapsid and may facilitate development of RSV antiviral therapy.
History
DepositionMar 24, 2023-
Header (metadata) releaseSep 6, 2023-
Map releaseSep 6, 2023-
UpdateSep 6, 2023-
Current statusSep 6, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35728.png

Downloads & links

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Map

FileDownload / File: emd_35728.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.135
Minimum - Maximum-0.24929246 - 0.5243166
Average (Standard dev.)0.0067534894 (±0.023612333)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 374.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35728_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35728_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : respiratory syncytial virus nucleocapsid-like assembly

EntireName: respiratory syncytial virus nucleocapsid-like assembly
Components
  • Complex: respiratory syncytial virus nucleocapsid-like assembly
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (35-MER)

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Supramolecule #1: respiratory syncytial virus nucleocapsid-like assembly

SupramoleculeName: respiratory syncytial virus nucleocapsid-like assembly
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human respiratory syncytial virus A

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Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Human respiratory syncytial virus A
Molecular weightTheoretical: 40.198215 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 LKENGV

UniProtKB: Nucleoprotein

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Macromolecule #2: RNA (35-MER)

MacromoleculeName: RNA (35-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.670844 KDa
SequenceString:
UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUU

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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 / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.6 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42956

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