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- EMDB-51640: Subtomogram average of immature Langat virus from cryo-electron t... -

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Entry
Database: EMDB / ID: EMD-51640
TitleSubtomogram average of immature Langat virus from cryo-electron tomograms of infected cells
Map dataSubtomogram average of immature Langat virus from cryo-electron tomograms of infected cells
Sample
  • Virus: Langat virus
Keywordsflavivirus / VIRUS
Biological speciesLangat virus
Methodsubtomogram averaging / cryo EM / Resolution: 33.0 Å
AuthorsCarlson LA / Dahmane S
Funding support France, Sweden, European Union, 5 items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)CDA00047/2017-C France
Swedish Research Council2018-05851 Sweden
Swedish Research Council2021-01145 Sweden
Swedish Research Council2023-02664 Sweden
H2020 Marie Curie Actions of the European Commission795892European Union
CitationJournal: bioRxiv / Year: 2024
Title: Cryo-electron tomography reveals coupled flavivirus replication, budding and maturation.
Authors: Selma Dahmane / Erin Schexnaydre / Jianguo Zhang / Ebba Rosendal / Nunya Chotiwan / Bina Kumari Singh / Wai-Lok Yau / Richard Lundmark / Benjamin Barad / Danielle A Grotjahn / Susanne Liese ...Authors: Selma Dahmane / Erin Schexnaydre / Jianguo Zhang / Ebba Rosendal / Nunya Chotiwan / Bina Kumari Singh / Wai-Lok Yau / Richard Lundmark / Benjamin Barad / Danielle A Grotjahn / Susanne Liese / Andreas Carlson / Anna K Överby / Lars-Anders Carlson /
Abstract: Flaviviruses replicate their genomes in replication organelles (ROs) formed as bud-like invaginations on the endoplasmic reticulum (ER) membrane, which also functions as the site for virion assembly. ...Flaviviruses replicate their genomes in replication organelles (ROs) formed as bud-like invaginations on the endoplasmic reticulum (ER) membrane, which also functions as the site for virion assembly. While this localization is well established, it is not known to what extent viral membrane remodeling, genome replication, virion assembly, and maturation are coordinated. Here, we imaged tick-borne flavivirus replication in human cells using cryo-electron tomography. We find that the RO membrane bud is shaped by a combination of a curvature-establishing coat and the pressure from intraluminal template RNA. A protein complex at the RO base extends to an adjacent membrane, where immature virions bud. Naturally occurring furin site variants determine whether virions mature in the immediate vicinity of ROs. We further visualize replication in mouse brain tissue by cryo-electron tomography. Taken together, these findings reveal a close spatial coupling of flavivirus genome replication, budding, and maturation.
History
DepositionSep 25, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51640.png

Downloads & links

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Map

FileDownload / File: emd_51640.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of immature Langat virus from cryo-electron tomograms of infected cells
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
10 Å/pix.
x 80 pix.
= 800. Å		10 Å/pix.
x 80 pix.
= 800. Å		10 Å/pix.
x 80 pix.
= 800. Å

Surface

Projections

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Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 10 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-1.2637429 - 1.7834225
Average (Standard dev.)0.008707484 (±0.34196433)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 800.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51640_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: half map 2

Fileemd_51640_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_51640_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Langat virus

EntireName: Langat virus
Components
  • Virus: Langat virus

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Supramolecule #1: Langat virus

SupramoleculeName: Langat virus / type: virus / ID: 1 / Parent: 0
Details: Cryo-electron tomograms of A549 cells infected with Langat virus
NCBI-ID: 11085 / Sci species name: Langat virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: tick (unknown)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE
DetailsA549 cells infected with Langat virus

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 2.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 33.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 84
ExtractionNumber tomograms: 11 / Number images used: 84 / Reference model: one particle from the data set
Final angle assignmentType: ANGULAR RECONSTITUTION

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