+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22164 | ||||||||||||
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Title | Assembly intermediates of orthoreovirus captured in the cell | ||||||||||||
Map data | DLP pseudo 6-fold | ||||||||||||
Sample |
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Function / homology | Function and homology information host cell surface binding / symbiont-mediated suppression of host PKR/eIFalpha signaling / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / protein serine/threonine kinase inhibitor activity / host cell endoplasmic reticulum / host cell mitochondrion / viral life cycle / viral capsid ...host cell surface binding / symbiont-mediated suppression of host PKR/eIFalpha signaling / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / protein serine/threonine kinase inhibitor activity / host cell endoplasmic reticulum / host cell mitochondrion / viral life cycle / viral capsid / regulation of translation / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / apoptotic process / host cell plasma membrane / structural molecule activity / RNA binding / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Mammalian orthoreovirus 3 Dearing | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 5.6 Å | ||||||||||||
Authors | Sutton G / Sun DP / Fu XF / Kotecha A / Hecksel GW / Clare DK / Zhang P / Stuart D / Boyce M | ||||||||||||
Funding support | United Kingdom, United States, 3 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Assembly intermediates of orthoreovirus captured in the cell. Authors: Geoff Sutton / Dapeng Sun / Xiaofeng Fu / Abhay Kotecha / Corey W Hecksel / Daniel K Clare / Peijun Zhang / David I Stuart / Mark Boyce / Abstract: Traditionally, molecular assembly pathways for viruses are inferred from high resolution structures of purified stable intermediates, low resolution images of cell sections and genetic approaches. ...Traditionally, molecular assembly pathways for viruses are inferred from high resolution structures of purified stable intermediates, low resolution images of cell sections and genetic approaches. Here, we directly visualise an unsuspected 'single shelled' intermediate for a mammalian orthoreovirus in cryo-preserved infected cells, by cryo-electron tomography of cellular lamellae. Particle classification and averaging yields structures to 5.6 Å resolution, sufficient to identify secondary structural elements and produce an atomic model of the intermediate, comprising 120 copies each of protein λ1 and σ2. This λ1 shell is 'collapsed' compared to the mature virions, with molecules pushed inwards at the icosahedral fivefolds by ~100 Å, reminiscent of the first assembly intermediate of certain prokaryotic dsRNA viruses. This supports the supposition that these viruses share a common ancestor, and suggests mechanisms for the assembly of viruses of the Reoviridae. Such methodology holds promise for dissecting the replication cycle of many viruses. #1: Journal: bioRxiv / Year: 2020 Title: Assembly intermediates of orthoreovirus captured in the cell Authors: Sutton G / Sun DP / Fu XF / Kotecha A / Hecksel GW / Clare DK / Zhang P / Stuart D / Boyce M | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22164.map.gz | 6.7 MB | EMDB map data format | |
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Header (meta data) | emd-22164-v30.xml emd-22164.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
Images | emd_22164.png | 87.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22164 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22164 | HTTPS FTP |
-Validation report
Summary document | emd_22164_validation.pdf.gz | 78.2 KB | Display | EMDB validaton report |
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Full document | emd_22164_full_validation.pdf.gz | 77.3 KB | Display | |
Data in XML | emd_22164_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22164 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22164 | HTTPS FTP |
-Related structure data
Related structure data | 6ztyMC 6xf7C 6xf8C 6ztsC 6ztzC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_22164.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | DLP pseudo 6-fold | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : reovirus SLP
Entire | Name: reovirus SLP |
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Components |
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-Supramolecule #1: reovirus SLP
Supramolecule | Name: reovirus SLP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Mammalian orthoreovirus 3 Dearing |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 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: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: emClarity / Number subtomograms used: 3039 |
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Extraction | Number tomograms: 4 / Number images used: 3039 |
Final angle assignment | Type: OTHER |
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | PDB-6zty: |