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- EMDB-33405: icosahedral reconstruction of mud crab reovirus in transcriptiona... -

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Entry
Database: EMDB / ID: EMD-33405
Titleicosahedral reconstruction of mud crab reovirus in transcriptionally active state
Map dataStructure of tMCRV with icos symmetry
Sample
  • Virus: Scylla serrata reovirus SZ-2007
Biological speciesScylla serrata reovirus SZ-2007
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhang Q / Gao Y
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31570736 China
National Natural Science Foundation of China (NSFC)31672677 China
CitationJournal: PLoS Pathog / Year: 2023
Title: The structure of a 12-segmented dsRNA reovirus: New insights into capsid stabilization and organization.
Authors: Qinfen Zhang / Yuanzhu Gao / Matthew L Baker / Shanshan Liu / Xudong Jia / Haidong Xu / Jianguo He / Jason T Kaelber / Shaoping Weng / Wen Jiang /
Abstract: Infecting a wide range of hosts, members of Reovirales (formerly Reoviridae) consist of a genome with different numbers of segmented double stranded RNAs (dsRNA) encapsulated by a proteinaceous shell ...Infecting a wide range of hosts, members of Reovirales (formerly Reoviridae) consist of a genome with different numbers of segmented double stranded RNAs (dsRNA) encapsulated by a proteinaceous shell and carry out genome replication and transcription inside the virion. Several cryo-electron microscopy (cryo-EM) structures of reoviruses with 9, 10 or 11 segmented dsRNA genomes have revealed insights into genome arrangement and transcription. However, the structure and genome arrangement of 12-segmented Reovirales members remain poorly understood. Using cryo-EM, we determined the structure of mud crab reovirus (MCRV), a 12-segmented dsRNA virus that is a putative member of Reovirales in the non-turreted Sedoreoviridae family, to near-atomic resolutions with icosahedral symmetry (3.1 Å) and without imposing icosahedral symmetry (3.4 Å). These structures revealed the organization of the major capsid proteins in two layers: an outer T = 13 layer consisting of VP12 trimers and unique VP11 clamps, and an inner T = 1 layer consisting of VP3 dimers. Additionally, ten RNA dependent RNA polymerases (RdRp) were well resolved just below the VP3 layer but were offset from the 5-fold axes and arranged with D5 symmetry, which has not previously been seen in other members of Reovirales. The N-termini of VP3 were shown to adopt four unique conformations; two of which anchor the RdRps, while the other two conformations are likely involved in genome organization and capsid stability. Taken together, these structures provide a new level of understanding for capsid stabilization and genome organization of segmented dsRNA viruses.
History
DepositionMay 9, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateMay 24, 2023-
Current statusMay 24, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33405.png

Downloads & links

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Map

FileDownload / File: emd_33405.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of tMCRV with icos symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 800 pix.
= 872. Å		1.09 Å/pix.
x 800 pix.
= 872. Å		1.09 Å/pix.
x 800 pix.
= 872. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-3.6546092 - 5.62735
Average (Standard dev.)0.0032955839 (±0.362775)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-400-400-400
Dimensions800800800
Spacing800800800
CellA=B=C: 872.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 2

Fileemd_33405_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_33405_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Scylla serrata reovirus SZ-2007

EntireName: Scylla serrata reovirus SZ-2007
Components
  • Virus: Scylla serrata reovirus SZ-2007

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Supramolecule #1: Scylla serrata reovirus SZ-2007

SupramoleculeName: Scylla serrata reovirus SZ-2007 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 458682 / Sci species name: Scylla serrata reovirus SZ-2007 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Scylla serrata (giant mud crab)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.6 µm / Calibrated magnification: 128440 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21945
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: jspr (ver. 2014)

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