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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


icosahedral viral capsid / host cell surface binding / viral inner capsid / symbiont-mediated suppression of host PKR/eIFalpha signaling / viral outer capsid / symbiont entry into host cell via permeabilization of host membrane / host cell endoplasmic reticulum / protein serine/threonine kinase inhibitor activity / 7-methylguanosine mRNA capping / host cell mitochondrion ...icosahedral viral capsid / host cell surface binding / viral inner capsid / symbiont-mediated suppression of host PKR/eIFalpha signaling / viral outer capsid / symbiont entry into host cell via permeabilization of host membrane / host cell endoplasmic reticulum / protein serine/threonine kinase inhibitor activity / 7-methylguanosine mRNA capping / host cell mitochondrion / viral life cycle / viral capsid / regulation of translation / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / symbiont-mediated suppression of host innate immune response / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / GTP binding / host cell plasma membrane / structural molecule activity / ATP hydrolysis activity / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Mu1 membrane penetration protein, domain I / Reovirus, outer capsid sigma 3 / Reovirus, outer capsid sigma-3 domain superfamily / Reovirus outer capsid protein, Sigma 3 / Outer capsid protein Mu1/VP4 / Mu1 membrane penetration protein, domain IV / Mu1 membrane penetration protein, domain II / Mu1/VP4 superfamily / Mu1 membrane penetration protein, domain III / Reovirus major virion structural protein Mu-1/Mu-1C (M2) ...Mu1 membrane penetration protein, domain I / Reovirus, outer capsid sigma 3 / Reovirus, outer capsid sigma-3 domain superfamily / Reovirus outer capsid protein, Sigma 3 / Outer capsid protein Mu1/VP4 / Mu1 membrane penetration protein, domain IV / Mu1 membrane penetration protein, domain II / Mu1/VP4 superfamily / Mu1 membrane penetration protein, domain III / Reovirus major virion structural protein Mu-1/Mu-1C (M2) / Sigma1/sigma2, reoviral / Reoviral Sigma1/Sigma2 family / : / : / : / : / : / : / : / : / Reovirus core-spike protein lambda-2 (L2), 6th domain / Reovirus core-spike protein lambda-2 (L2), 7th domain / Reovirus core-spike protein lambda-2 (L2), ferredoxin-like domain / Reovirus core-spike protein lambda-2 (L2), GTase domain / Reovirus core-spike protein lambda-2 (L2), N-terminal / Reovirus core-spike protein lambda-2 (L2), methyltransferase-1 / Reovirus core-spike protein lambda-2 (L2), methyltransferase-2 / : / Inner capsid protein lambda-1/VP3 / Reovirus core-spike lambda-2 / Reovirus core-spike protein lambda-2 (L2), C-terminal / Inner capsid protein lambda-1/ VP3 / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
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
Similarity search - Component
Biological speciesReovirus sp.
MethodELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 6.5 Å
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.
History
DepositionJul 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 2, 2025Group: Data processing / Structure summary / Category: em_3d_reconstruction / pdbx_entry_details
Item: _em_3d_reconstruction.num_particles / _em_3d_reconstruction.resolution / _em_3d_reconstruction.resolution_method

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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
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
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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Details

Has protein modificationN

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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: all / 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 reconstructionResolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF
Atomic model buildingProtocol: FLEXIBLE FIT

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