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- PDB-6ztz: Assembly intermediates of orthoreovirus captured in the cell -

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Basic information

Entry
Database: PDB / ID: 6ztz
TitleAssembly intermediates of orthoreovirus captured in the cell
Components
  • (Inner capsid protein lambda- ...) x 2
  • (Outer capsid protein ...) x 3
  • Inner capsid protein sigma-2
KeywordsVIRUS LIKE PARTICLE / Assemble Intermediates / Orthoreovirus / cryo-electron tomography / cellular lamellae
Function / homology
Function and homology information


mRNA guanylyltransferase activity / mRNA guanylyltransferase / icosahedral viral capsid / viral inner capsid / 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 ...mRNA guanylyltransferase activity / mRNA guanylyltransferase / icosahedral viral capsid / viral inner capsid / 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 / mRNA (guanine-N7)-methyltransferase / 7-methylguanosine mRNA capping / host cell endoplasmic reticulum / mRNA (guanine-N7-)-methyltransferase activity / viral life cycle / viral capsid / regulation of translation / suppression by virus of host type I interferon-mediated signaling pathway / RNA helicase / RNA helicase activity / pathogenesis / host cell plasma membrane / GTP binding / structural molecule activity / RNA binding / membrane / ATP binding / metal ion binding
Reovirus core-spike lambda-2 / Mu1/VP4 superfamily / Reovirus, outer capsid sigma-3 domain superfamily / Mu1 membrane penetration protein, subdomain 2 / Mu1 membrane penetration protein, subdomain 1 / Mu1 membrane penetration protein, subdomain 3 / Immunoglobulin-like fold / Zinc finger C2H2-type / Outer capsid protein Mu1/VP4 / Sigma1/sigma2, reoviral / Reovirus, outer capsid sigma 3
Outer capsid protein sigma-3 / Outer capsid protein mu-1 / Outer capsid protein lambda-2 / Inner capsid protein sigma-2 / Inner capsid protein lambda-1
Biological speciesReovirus sp.
MethodELECTRON MICROSCOPY / electron tomography / cryo EM
AuthorsSutton, G.C. / Stuart, D.I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
Wellcome Trust206422/Z/17/Z United Kingdom
CitationJournal: 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
SummaryFull reportAbout validation report
History
DepositionJul 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
B: Inner capsid protein lambda-1
C: Inner capsid protein lambda-1
D: Inner capsid protein sigma-2
K: Outer capsid protein mu-1
L: Outer capsid protein mu-1
M: Outer capsid protein mu-1
O: Outer capsid protein lambda-2
P: Inner capsid protein sigma-2
X: Outer capsid protein sigma-3
Y: Outer capsid protein sigma-3
Z: Outer capsid protein sigma-3


Theoretical massNumber of molelcules
Total (without water)798,77311
Polymers798,77311
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area51250 Å2
ΔGint-228 kcal/mol
Surface area341860 Å2

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Components

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Inner capsid protein lambda- ... , 2 types, 2 molecules BC

#1: Protein Inner capsid protein lambda-1 / Lambda 1


Mass: 116214.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Reovirus sp. / References: UniProt: Q9WAB2
#2: Protein Inner capsid protein lambda-1 / Lambda 1


Mass: 113187.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Reovirus sp. / References: UniProt: Q9WAB2

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Protein , 1 types, 2 molecules DP

#3: Protein Inner capsid protein sigma-2 / Sigma 2


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 Outer capsid protein mu-1 / Mu1


Mass: 69315.602 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Reovirus sp. / References: UniProt: P11077
#5: Protein Outer capsid protein lambda-2 / Lambda 2


Mass: 143665.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Reovirus sp. / References: UniProt: P11079
#6: Protein Outer capsid protein sigma-3 / Sigma 3


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: electron tomography

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Sample preparation

ComponentName: 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: #1-#6 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Reovirus sp.
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER
Image recordingElectron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionNum. of particles: 41
Atomic model buildingProtocol: FLEXIBLE FIT

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