+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4867 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Sub-tomogram averaging of Tula virus glycoprotein spike | |||||||||
Map data | Sub-tomogram averaging of Tula virus glycoprotein spike with corrected hand | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / endocytosis involved in viral entry into host cell / host cell surface / host cell endoplasmic reticulum membrane / induction by virus of host autophagy / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane ...symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / endocytosis involved in viral entry into host cell / host cell surface / host cell endoplasmic reticulum membrane / induction by virus of host autophagy / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / signal transduction / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Tula orthohantavirus | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 15.6 Å | |||||||||
Authors | Huiskonen JT / Stass R / Li S | |||||||||
Citation | Journal: Cell / Year: 2020 Title: The Hantavirus Surface Glycoprotein Lattice and Its Fusion Control Mechanism. Authors: Alexandra Serris / Robert Stass / Eduardo A Bignon / Nicolás A Muena / Jean-Claude Manuguerra / Rohit K Jangra / Sai Li / Kartik Chandran / Nicole D Tischler / Juha T Huiskonen / Felix A ...Authors: Alexandra Serris / Robert Stass / Eduardo A Bignon / Nicolás A Muena / Jean-Claude Manuguerra / Rohit K Jangra / Sai Li / Kartik Chandran / Nicole D Tischler / Juha T Huiskonen / Felix A Rey / Pablo Guardado-Calvo / Abstract: Hantaviruses are rodent-borne viruses causing serious zoonotic outbreaks worldwide for which no treatment is available. Hantavirus particles are pleomorphic and display a characteristic square ...Hantaviruses are rodent-borne viruses causing serious zoonotic outbreaks worldwide for which no treatment is available. Hantavirus particles are pleomorphic and display a characteristic square surface lattice. The envelope glycoproteins Gn and Gc form heterodimers that further assemble into tetrameric spikes, the lattice building blocks. The glycoproteins, which are the sole targets of neutralizing antibodies, drive virus entry via receptor-mediated endocytosis and endosomal membrane fusion. Here we describe the high-resolution X-ray structures of the heterodimer of Gc and the Gn head and of the homotetrameric Gn base. Docking them into an 11.4-Å-resolution cryoelectron tomography map of the hantavirus surface accounted for the complete extramembrane portion of the viral glycoprotein shell and allowed a detailed description of the surface organization of these pleomorphic virions. Our results, which further revealed a built-in mechanism controlling Gc membrane insertion for fusion, pave the way for immunogen design to protect against pathogenic hantaviruses. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4867.map.gz | 14.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-4867-v30.xml emd-4867.xml | 7.8 KB 7.8 KB | Display Display | EMDB header |
Images | emd_4867.png | 70.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4867 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4867 | HTTPS FTP |
-Validation report
Summary document | emd_4867_validation.pdf.gz | 237.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_4867_full_validation.pdf.gz | 236.4 KB | Display | |
Data in XML | emd_4867_validation.xml.gz | 5.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4867 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4867 | HTTPS FTP |
-Related structure data
Related structure data | 6y5fC 6y5wC 6y62C 6y68C 6y6pC 6y6qC 6yrbC 6yrqC 6zjmC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_4867.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sub-tomogram averaging of Tula virus glycoprotein spike with corrected hand | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Tula orthohantavirus
Entire | Name: Tula orthohantavirus |
---|---|
Components |
|
-Supramolecule #1: Tula orthohantavirus
Supramolecule | Name: Tula orthohantavirus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1980494 / Sci species name: Tula orthohantavirus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No |
---|
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 15.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 5449 |
---|---|
Extraction | Number tomograms: 30 / Number images used: 5449 |
Final angle assignment | Type: OTHER |