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- PDB-9cyy: Cryo-EM structure of MRV virion -

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Basic information

Entry
Database: PDB / ID: 9cyy
TitleCryo-EM structure of MRV virion
Components
  • (Outer capsid protein ...) x 3
  • Inner capsid protein sigma-2
  • Lambda 1
  • Mu2
  • RNA-directed RNA polymerase
KeywordsVIRAL PROTEIN / Mammalian reovirus / outer shell
Function / homology
Function and homology information


icosahedral viral capsid / host cell surface binding / viral inner capsid / symbiont-mediated suppression of host PKR/eIFalpha signaling / host cytoskeleton / viral outer capsid / symbiont entry into host cell via permeabilization of host membrane / protein serine/threonine kinase inhibitor activity / host cell endoplasmic reticulum / 7-methylguanosine mRNA capping ...icosahedral viral capsid / host cell surface binding / viral inner capsid / symbiont-mediated suppression of host PKR/eIFalpha signaling / host cytoskeleton / viral outer capsid / symbiont entry into host cell via permeabilization of host membrane / protein serine/threonine kinase inhibitor activity / host cell endoplasmic reticulum / 7-methylguanosine mRNA capping / host cell mitochondrion / viral life cycle / viral genome replication / viral capsid / regulation of translation / mRNA guanylyltransferase activity / viral nucleocapsid / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / hydrolase activity / RNA helicase activity / RNA helicase / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTP binding / host cell nucleus / host cell plasma membrane / structural molecule 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 minor core protein, Mu-2 / Reovirus minor core protein Mu-2 / : / : / : / : / : / : / : / : / 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 / Reovirus RNA-dependent RNA polymerase lambda 3 / Reovirus RNA-dependent RNA polymerase lambda 3 / : / 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 / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulin-like fold / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
RNA-directed RNA polymerase / RNA helicase / Inner capsid protein sigma-2 / Outer capsid protein sigma-3 / Outer capsid protein mu-1 / Outer capsid protein lambda-2 / Mu2
Similarity search - Component
Biological speciesMammalian orthoreovirus 3 Dearing
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsLiu, X.Y. / Xia, X. / Martynowycz, M.W. / Gonen, T. / Zhou, Z.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
CitationJournal: Nat Commun / Year: 2024
Title: Molecular sociology of virus-induced cellular condensates supporting reovirus assembly and replication.
Authors: Xiaoyu Liu / Xian Xia / Michael W Martynowycz / Tamir Gonen / Z Hong Zhou /
Abstract: Virus-induced cellular condensates, or viral factories, are poorly understood high-density phases where replication of many viruses occurs. Here, by cryogenic electron tomography (cryoET) of focused ...Virus-induced cellular condensates, or viral factories, are poorly understood high-density phases where replication of many viruses occurs. Here, by cryogenic electron tomography (cryoET) of focused ion beam (FIB) milling-produced lamellae of mammalian reovirus (MRV)-infected cells, we visualized the molecular organization and interplay (i.e., "molecular sociology") of host and virus in 3D at two time points post-infection, enabling a detailed description of these condensates and a mechanistic understanding of MRV replication within them. Expanding over time, the condensate fashions host ribosomes at its periphery, and host microtubules, lipid membranes, and viral molecules in its interior, forming a 3D architecture that supports the dynamic processes of viral genome replication and capsid assembly. A total of six MRV assembly intermediates are identified inside the condensate: star core, empty and genome-containing cores, empty and full virions, and outer shell particle. Except for star core, these intermediates are visualized at atomic resolution by cryogenic electron microscopy (cryoEM) of cellular extracts. The temporal sequence and spatial rearrangement among these viral intermediates choreograph the viral life cycle within the condensates. Together, the molecular sociology of MRV-induced cellular condensate highlights the functional advantage of transient enrichment of molecules at the right location and time for viral replication.
History
DepositionAug 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Inner capsid protein sigma-2
A: Outer capsid protein mu-1
B: Outer capsid protein mu-1
C: Inner capsid protein sigma-2
D: Outer capsid protein mu-1
E: Outer capsid protein mu-1
F: Outer capsid protein mu-1
G: Outer capsid protein sigma-3
H: Outer capsid protein mu-1
I: Outer capsid protein sigma-3
J: Outer capsid protein lambda-2
K: Lambda 1
L: Outer capsid protein sigma-3
M: Lambda 1
V: Mu2
W: RNA-directed RNA polymerase
Y: Lambda 1
Z: Lambda 1
a: Lambda 1
b: Lambda 1
c: Lambda 1
d: Lambda 1
e: Lambda 1
f: Lambda 1
g: Lambda 1
h: Lambda 1
i: Lambda 1
k: Lambda 1
m: Lambda 1


Theoretical massNumber of molelcules
Total (without water)3,174,86229
Polymers3,174,86229
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 19 molecules 0CKMYZabcdefghikmVW

#1: Protein Inner capsid protein sigma-2 / Sigma2


Mass: 47206.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 Dearing / References: UniProt: P03525
#5: Protein
Lambda 1 / Lambda1


Mass: 141937.375 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 Dearing / References: UniProt: F1ARN3
#6: Protein Mu2 / Mu 2


Mass: 83331.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 Dearing / References: UniProt: Q6EDZ8
#7: Protein RNA-directed RNA polymerase


Mass: 142449.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 Dearing
References: UniProt: A0A0B5CSU4, RNA-directed RNA polymerase

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Outer capsid protein ... , 3 types, 10 molecules ABDEFHGILJ

#2: Protein
Outer capsid protein mu-1 / Mu1


Mass: 76334.273 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 Dearing / References: UniProt: P11078
#3: Protein Outer capsid protein sigma-3 / Sigma3


Mass: 41168.121 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 Dearing / References: UniProt: P03527
#4: Protein Outer capsid protein lambda-2 / Lambda2 / Lambda2(Cap)


Mass: 144098.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 Dearing
References: UniProt: P11079, mRNA guanylyltransferase, mRNA (guanine-N7)-methyltransferase

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mammalian orthoreovirus 3 Dearing / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Mammalian orthoreovirus 3 Dearing
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: LLC-MK2
Buffer solutionpH: 7.4 / Details: Phosphate-buffered saline
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 22739
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2SerialEM4.1image acquisition
4CTFFIND4.1CTF correction
9PHENIX1.19model refinement
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 592105
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97187 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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