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Yorodumi- PDB-8op2: Stacks of nucleocapsid rings of the N1-370 mutant of the human Re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8op2 | ||||||
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Title | Stacks of nucleocapsid rings of the N1-370 mutant of the human Respiratory Syncytial Virus | ||||||
Components |
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Keywords | VIRAL PROTEIN / N-RNA / nucleoprotein / nucleocapsid / RSV | ||||||
Function / homology | Function and homology information Respiratory syncytial virus genome transcription / symbiont-mediated suppression of host PKR/eIFalpha signaling / Translation of respiratory syncytial virus mRNAs / Respiratory syncytial virus (RSV) attachment and entry / 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 genome transcription / symbiont-mediated suppression of host PKR/eIFalpha signaling / Translation of respiratory syncytial virus mRNAs / Respiratory syncytial virus (RSV) attachment and entry / 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 / 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 / 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 | ||||||
Biological species | Human respiratory syncytial virus A strain Long Trichoplusia ni (cabbage looper) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Gonnin, L. / Desfosses, A. / Gutsche, I. | ||||||
Funding support | France, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8op2.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8op2.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 8op2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8op2_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8op2_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8op2_validation.xml.gz | 173 KB | Display | |
Data in CIF | 8op2_validation.cif.gz | 268.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/8op2 ftp://data.pdbj.org/pub/pdb/validation_reports/op/8op2 | HTTPS FTP |
-Related structure data
Related structure data | 17038MC 8oouC 8op1C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 41116.254 Da / Num. of mol.: 20 Source method: isolated from a genetically manipulated source Details: C-terminally truncated mutant of the nucleoprotein N of human RSV (N1-370) Source: (gene. exp.) Human respiratory syncytial virus A strain Long Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03418 #2: RNA chain | Mass: 21317.777 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trichoplusia ni (cabbage looper) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Stacks of nucleocapsid rings of the N1-370 mutant of the Respiratory Syncytial Virus Type: COMPLEX Details: Stacks of nucleocapsid rings formed by the C-terminallt truncated nucleoprotein (N1-370) of the human respiratory syncytial virus upon overexpression in insect cells and non specific ...Details: Stacks of nucleocapsid rings 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 Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Human respiratory syncytial virus A strain Long |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) / Strain: High Five / Plasmid: pFastBac |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 42 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: D10 (2x10 fold dihedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81918 / Symmetry type: POINT | ||||||||||||||||||||||||
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