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Yorodumi- EMDB-17038: Stacks of nucleocapsid rings of the N1-370 mutant of the human Re... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17038 | |||||||||
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Title | Stacks of nucleocapsid rings of the N1-370 mutant of the human Respiratory Syncytial Virus | |||||||||
Map data | Stacks of nucleocapsid rings of the N1-370 mutant of the Respiratory Syncytial Virus | |||||||||
Sample |
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Keywords | N-RNA / nucleoprotein / nucleocapsid / RSV / VIRAL PROTEIN | |||||||||
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 / 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 / symbiont-mediated suppression of host PKR/eIFalpha signaling / Translation of respiratory syncytial virus mRNAs / 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 / 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 | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Gonnin L / Desfosses A / Gutsche I | |||||||||
Funding support | France, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17038.map.gz | 18.1 MB | EMDB map data format | |
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Header (meta data) | emd-17038-v30.xml emd-17038.xml | 16.1 KB 16.1 KB | Display Display | EMDB header |
Images | emd_17038.png | 170.1 KB | ||
Others | emd_17038_half_map_1.map.gz emd_17038_half_map_2.map.gz | 226.4 MB 226.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17038 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17038 | HTTPS FTP |
-Related structure data
Related structure data | 8op2MC 8oouC 8op1C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17038.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Stacks of nucleocapsid rings of the N1-370 mutant of the Respiratory Syncytial Virus | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.145 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Stacks of nucleocapsid rings of the N1-370 mutant...
File | emd_17038_half_map_1.map | ||||||||||||
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Annotation | Stacks of nucleocapsid rings of the N1-370 mutant of the Respiratory Syncytial Virus. Half B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Stacks of nucleocapsid rings of the N1-370 mutant...
File | emd_17038_half_map_2.map | ||||||||||||
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Annotation | Stacks of nucleocapsid rings of the N1-370 mutant of the Respiratory Syncytial Virus. Half A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Stacks of nucleocapsid rings of the N1-370 mutant of the Respirat...
Entire | Name: Stacks of nucleocapsid rings of the N1-370 mutant of the Respiratory Syncytial Virus |
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Components |
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-Supramolecule #1: Stacks of nucleocapsid rings of the N1-370 mutant of the Respirat...
Supramolecule | Name: Stacks of nucleocapsid rings of the N1-370 mutant of the Respiratory Syncytial Virus type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 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 |
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Source (natural) | Organism: Human respiratory syncytial virus A strain Long |
-Macromolecule #1: Nucleoprotein
Macromolecule | Name: Nucleoprotein / type: protein_or_peptide / ID: 1 Details: C-terminally truncated mutant of the nucleoprotein N of human RSV (N1-370) Number of copies: 20 / Enantiomer: LEVO |
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Source (natural) | Organism: Human respiratory syncytial virus A strain Long |
Molecular weight | Theoretical: 41.116254 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: 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 VLDL UniProtKB: Nucleoprotein |
-Macromolecule #2: RNA (70-mer)
Macromolecule | Name: RNA (70-mer) / type: rna / ID: 2 / Number of copies: 2 |
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Source (natural) | Organism: Trichoplusia ni (cabbage looper) |
Molecular weight | Theoretical: 21.317777 KDa |
Sequence | String: CCCCCCCCCC CCCCCCCCCC CCCCCCCCCC CCCCCCCCCC CCCCCCCCCC CCCCCCCCCC CCCCCCCCCC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.7000000000000001 µm |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: D10 (2x10 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81918 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |