+Open data
-Basic information
Entry | Database: PDB / ID: 6xf7 | ||||||||||||
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Title | SLP | ||||||||||||
Components | Lambda 1 protein | ||||||||||||
Keywords | VIRUS 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 | ||||||||||||
Biological species | Mammalian orthoreovirus | ||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 6.6 Å | ||||||||||||
Authors | Sutton, 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
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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. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6xf7.cif.gz | 390.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xf7.ent.gz | 309.9 KB | Display | PDB format |
PDBx/mmJSON format | 6xf7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xf7_validation.pdf.gz | 818.5 KB | Display | wwPDB validaton report |
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Full document | 6xf7_full_validation.pdf.gz | 996.9 KB | Display | |
Data in XML | 6xf7_validation.xml.gz | 84 KB | Display | |
Data in CIF | 6xf7_validation.cif.gz | 120.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/6xf7 ftp://data.pdbj.org/pub/pdb/validation_reports/xf/6xf7 | HTTPS FTP |
-Related structure data
Related structure data | 22165MC 6xf8C 6ztsC 6ztyC 6ztzC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: reovirus SLP / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Mammalian orthoreovirus 3 Dearing |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software | Name: emClarity / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C5 (5 fold cyclic) |
3D reconstruction | Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2683 / Symmetry type: POINT |
EM volume selection | Num. of tomograms: 4 / Num. of volumes extracted: 2683 |
Atomic model building | Protocol: FLEXIBLE FIT |