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- EMDB-31617: Cryo-EM map of GETV 2-fold axis -

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Basic information

Entry
Database: EMDB / ID: EMD-31617
TitleCryo-EM map of GETV 2-fold axis
Map data
Sample
  • Virus: Getah virus
Biological speciesGetah virus
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 2.85 Å
AuthorsLiu Z / Liu C / Wang A
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81870246 China
National Natural Science Foundation of China (NSFC)82070329 China
CitationJournal: Cell Discov / Year: 2022
Title: Structure of infective Getah virus at 2.8 Å resolution determined by cryo-electron microscopy.
Authors: Aojie Wang / Feng Zhou / Congcong Liu / Dongsheng Gao / Ruxi Qi / Yiheng Yin / Sheng Liu / Yuanzhu Gao / Lutang Fu / Yinhe Xia / Yawei Xu / Chuanqing Wang / Zheng Liu /
Abstract: Getah virus (GETV), a member of the genus alphavirus, is a mosquito-borne pathogen that can cause pyrexia and reproductive losses in animals. Although antibodies to GETV have been found in over 10% ...Getah virus (GETV), a member of the genus alphavirus, is a mosquito-borne pathogen that can cause pyrexia and reproductive losses in animals. Although antibodies to GETV have been found in over 10% of healthy people, there are no reports of clinical symptoms associated with GETV. The biological and pathological properties of GETV are largely unknown and antiviral or vaccine treatments against GETV are still unavailable due to a lack of knowledge of the structure of the GETV virion. Here, we present the structure of infective GETV at a resolution of 2.8 Å with the atomic models of the capsid protein and the envelope glycoproteins E1 and E2. We have identified numerous glycosylation and S-acylation sites in E1 and E2. The surface-exposed glycans indicate a possible impact on viral immune evasion and host cell invasion. The S-acylation sites might be involved in stabilizing the transmembrane assembly of E1 and E2. In addition, a cholesterol and a phospholipid molecule are observed in a transmembrane hydrophobic pocket, together with two more cholesterols surrounding the pocket. The cholesterol and phospholipid stabilize the hydrophobic pocket in the viral envelope membrane. The structural information will assist structure-based antiviral and vaccine screening, design, and optimization.
History
DepositionAug 3, 2021-
Header (metadata) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateJun 15, 2022-
Current statusJun 15, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31617.png

Downloads & links

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Map

FileDownload / File: emd_31617.map.gz / Format: CCP4 / Size: 95 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 292 pix.
= 242.36 Å		0.83 Å/pix.
x 292 pix.
= 242.36 Å		0.83 Å/pix.
x 292 pix.
= 242.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0104
Minimum - Maximum-0.0448952 - 0.067334056
Average (Standard dev.)0.00039133822 (±0.0033457975)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions292292292
Spacing292292292
CellA=B=C: 242.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Getah virus

EntireName: Getah virus
Components
  • Virus: Getah virus

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Supramolecule #1: Getah virus

SupramoleculeName: Getah virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 59300 / Sci species name: Getah virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
StainingType: NEGATIVE / Material: Uranyl Acetate
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 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: 1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6013560
Details: The whole virus particles was selected from micrographs using EMAN2. And The particles were clipped using JSPR.
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Software - details: Relion reconstruction was used / Number images used: 2889370
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0.8)
Software - details: Relion reconstruction of cliped particles was used
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Software - details: Relion Refine3D was used to determin the final angular
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.0.8)
Software - details: Relion Class3D was used to remove the bad particles
FSC plot (resolution estimation)

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