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- PDB-6xf8: DLP 5 fold -

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Basic information

Entry
Database: PDB / ID: 6xf8
TitleDLP 5 fold
Components
  • Inner capsid protein lambda-1
  • Inner capsid protein sigma-2
  • Outer capsid protein mu-1
  • Outer capsid protein sigma-3
  • mRNA (guanine-N(7)-)-methyltransferase
KeywordsVIRUS LIKE PARTICLE / orthoreovirus
Function / homology
Function and homology information


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 ...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 / Inner capsid protein sigma-2 / Outer capsid protein lambda-2 / Inner capsid protein lambda-1
Similarity search - Component
Biological speciesReovirus type 1
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 6.5 Å
AuthorsSutton, G. / Sun, D.P. / Fu, X.F. / Kotecha, A. / Hecksel, G.W. / Clare, D.K. / Zhang, P. / Stuart, D. / Boyce, M.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
Wellcome Trust206422/Z/17/Z United Kingdom
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)GM082251 United States
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.
#1: Journal: To Be Published
Title: Assembly intermediates of orthoreovirus captured in the cell
Authors: Sutton, G. / Sun, D.P. / Fu, X.F. / Kotecha, A. / Hecksel, G.W. / Clare, D.K. / Zhang, P. / Stuart, D. / Boyce, M.
History
DepositionJun 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Assembly

Deposited unit
K: Outer capsid protein mu-1
I: Outer capsid protein sigma-3
H: Outer capsid protein sigma-3
G: Outer capsid protein sigma-3
F: Outer capsid protein mu-1
E: Inner capsid protein sigma-2
C: Inner capsid protein lambda-1
B: Inner capsid protein lambda-1
A: mRNA (guanine-N(7)-)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)689,8819
Polymers689,8819
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 68568.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Reovirus type 1 (strain Lang) / Strain: Lang / References: UniProt: P11077
#2: Protein Outer capsid protein sigma-3 / Sigma3


Mass: 41237.117 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Reovirus type 1 (strain Lang) / Strain: Lang / References: UniProt: P07939
#3: Protein Inner capsid protein sigma-2 / Sigma2


Mass: 47024.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Reovirus type 1 (strain Lang) / Strain: Lang / References: UniProt: P11314
#4: Protein Inner capsid protein lambda-1 / Lambda1 / ATP-dependent DNA helicase lambda-1 / Lambda1(Hel)


Mass: 119020.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Reovirus type 1 (strain Lang) / Strain: Lang / References: UniProt: Q9WAB2, RNA helicase
#5: Protein mRNA (guanine-N(7)-)-methyltransferase / mRNA guanylyltransferase


Mass: 143967.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Reovirus type 1 (strain Lang) / Strain: Lang
References: UniProt: Q91RA5, mRNA (guanine-N7)-methyltransferase, mRNA guanylyltransferase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: reovirus SLP / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Mammalian orthoreovirus 3 Dearing
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: emClarity / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 625 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 4 / Num. of volumes extracted: 625
Atomic model buildingProtocol: FLEXIBLE FIT

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