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Basic information

Entry
Database: PDB / ID: 6xf7
TitleSLP
ComponentsLambda 1 protein
KeywordsVIRUS LIKE PARTICLE
Function / homology
Function and homology information


viral inner capsid / 7-methylguanosine mRNA capping / RNA helicase activity / RNA helicase / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Inner capsid protein lambda-1/ VP3 / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Lambda 1 protein / Inner capsid protein lambda-1
Similarity search - Component
Biological speciesMammalian orthoreovirus
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 6.6 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
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
DepositionJun 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
B: Lambda 1 protein
C: Lambda 1 protein


Theoretical massNumber of molelcules
Total (without water)238,0412
Polymers238,0412
Non-polymers00
Water0
1


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

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Components

#1: Protein Lambda 1 protein /


Mass: 119020.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus / References: UniProt: A0A0E3JTF4, UniProt: Q9WAB2*PLUS

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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: all / 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 FIELDBright-field microscopy
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: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2683 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 4 / Num. of volumes extracted: 2683
Atomic model buildingProtocol: FLEXIBLE FIT

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