|Entry||Database: EMDB / ID: EMD-22164|
|Title||Assembly intermediates of orthoreovirus captured in the cell|
|Function / homology|
Function and homology information
host cell surface binding / viral outer capsid / viral entry via permeabilization of inner membrane / permeabilization of host organelle membrane involved in viral entry into host cell / suppression by virus of host PKR activity / host cell mitochondrion / host cell endoplasmic reticulum / viral life cycle / viral capsid / regulation of translation ...host cell surface binding / viral outer capsid / viral entry via permeabilization of inner membrane / permeabilization of host organelle membrane involved in viral entry into host cell / suppression by virus of host PKR activity / host cell mitochondrion / host cell endoplasmic reticulum / viral life cycle / viral capsid / regulation of translation / suppression by virus of host type I interferon-mediated signaling pathway / pathogenesis / host cell plasma membrane / structural molecule activity / RNA binding / membrane / metal ion binding
Mu1 membrane penetration protein, subdomain 1 / Mu1 membrane penetration protein, subdomain 3 / Outer capsid protein Mu1/VP4 / Mu1/VP4 superfamily / Reovirus, outer capsid sigma 3 / Reovirus, outer capsid sigma-3 domain superfamily / Mu1 membrane penetration protein, subdomain 2
Outer capsid protein sigma-3 / Outer capsid protein mu-1
|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 |
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.
|Validation Report||PDB-ID: 6zty|
SummaryFull reportAbout validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_22164.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.8 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire reovirus SLP
|Entire||Name: reovirus SLP / Number of components: 1|
-Component #1: protein, reovirus SLP
|Protein||Name: reovirus SLP / Recombinant expression: No|
|Source||Species: Mammalian orthoreovirus 3 Dearing|
|Specimen||Specimen state: Cell / Method: cryo EM|
|Sample solution||pH: 8|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: subtomogram averaging / Applied symmetry: C6 (6 fold cyclic) / Number of subtomograms: 3039|
|3D reconstruction||Software: emClarity / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
|Modeling #1||Refinement protocol: flexible|
-Aug 12, 2020. New: Covid-19 info
New: Covid-19 info
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info
+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi