+Open data
-Basic information
Entry | Database: PDB / ID: 6ztz | |||||||||
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Title | Assembly intermediates of orthoreovirus captured in the cell | |||||||||
Components |
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Keywords | VIRUS LIKE PARTICLE / Assemble Intermediates / Orthoreovirus / cryo-electron tomography / cellular lamellae | |||||||||
Function / homology | Function and homology information icosahedral viral capsid / host cell surface binding / viral inner capsid / 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 ...icosahedral viral capsid / host cell surface binding / viral inner capsid / 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 / 7-methylguanosine mRNA capping / viral life cycle / viral capsid / mRNA guanylyltransferase activity / regulation of translation / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / virus-mediated perturbation of host defense response / GTP binding / apoptotic process / host cell plasma membrane / structural molecule activity / ATP hydrolysis activity / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Reovirus sp. | |||||||||
Method | ELECTRON MICROSCOPY / electron tomography / cryo EM | |||||||||
Authors | Sutton, G.C. / Stuart, D.I. | |||||||||
Funding support | United Kingdom, 2items
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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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ztz.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ztz.ent.gz | 1012.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ztz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ztz_validation.pdf.gz | 778 KB | Display | wwPDB validaton report |
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Full document | 6ztz_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6ztz_validation.xml.gz | 241.9 KB | Display | |
Data in CIF | 6ztz_validation.cif.gz | 358.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/6ztz ftp://data.pdbj.org/pub/pdb/validation_reports/zt/6ztz | HTTPS FTP |
-Related structure data
Related structure data | 22166MC 6xf7C 6xf8C 6ztsC 6ztyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Inner capsid protein lambda- ... , 2 types, 2 molecules BC
#1: Protein | Mass: 116214.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Reovirus sp. / References: UniProt: Q9WAB2 |
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#2: Protein | Mass: 113187.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Reovirus sp. / References: UniProt: Q9WAB2 |
-Protein , 1 types, 2 molecules DP
#3: Protein | Mass: 47024.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Reovirus sp. / References: UniProt: P11314 |
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-Outer capsid protein ... , 3 types, 7 molecules KLMOXYZ
#4: Protein | Mass: 69315.602 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Reovirus sp. / References: UniProt: P11077 #5: Protein | | Mass: 143665.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Reovirus sp. / References: UniProt: P11079 #6: Protein | Mass: 41237.117 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Reovirus sp. / References: UniProt: P07939 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: electron tomography |
-Sample preparation
Component | Name: Inner capsid protein lambda-1, Inner capsid protein sigma-2, Outer capsid protein mu-1, Outer capsid protein lambda-2 and Outer capsid protein sigma-3 Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Reovirus sp. |
Details of virus | Empty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: NITROGEN |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: OTHER |
Image recording | Electron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Num. of particles: 41 |
Atomic model building | Protocol: FLEXIBLE FIT |