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- EMDB-17612: In-situ structure of the pentameric HEF trimers from influenza C ... -

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Basic information

Entry
Database: EMDB / ID: EMD-17612
TitleIn-situ structure of the pentameric HEF trimers from influenza C viral particles
Map data
Sample
  • Virus: Influenza C virus (C/Johannesburg/1/66)
KeywordsClass 1 fusion protein / membrane fusion / viral assembly / pentameric / VIRUS
Biological speciesInfluenza C virus (C/Johannesburg/1/66)
Methodsubtomogram averaging / cryo EM / Resolution: 12.2 Å
AuthorsLiu ZB / Rosenthal PB
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
CitationJournal: To Be Published
Title: Topological defects in the spherical virus crystal
Authors: Liu ZB / Rosenthal PB
History
DepositionJun 12, 2023-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17612.png

Downloads & links

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Map

FileDownload / File: emd_17612.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 256 pix.
= 353.28 Å		1.38 Å/pix.
x 256 pix.
= 353.28 Å		1.38 Å/pix.
x 256 pix.
= 353.28 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0372
Minimum - Maximum-0.09435956 - 0.1255331
Average (Standard dev.)0.00070027704 (±0.015439592)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 353.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17612_msk_1.map
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AxesZYX

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Histogram

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Half map: #1

Fileemd_17612_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17612_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Influenza C virus (C/Johannesburg/1/66)

EntireName: Influenza C virus (C/Johannesburg/1/66)
Components
  • Virus: Influenza C virus (C/Johannesburg/1/66)

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Supramolecule #1: Influenza C virus (C/Johannesburg/1/66)

SupramoleculeName: Influenza C virus (C/Johannesburg/1/66) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Purified viruses / NCBI-ID: 100673 / Sci species name: Influenza C virus (C/Johannesburg/1/66) / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Molecular weightTheoretical: 1.03 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMTRISTris
150.0 mMNaClSodium chloride
10.0 mMCaCl2Calcium chloride
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AMYLAMINE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III
DetailsHeterogeneous mix of viral particles, viral like particles and cellular vesicles

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number real images: 1 / Average exposure time: 1.1 sec. / Average electron dose: 2.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 64000
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

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 12.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number subtomograms used: 3108
ExtractionNumber tomograms: 83 / Number images used: 83 / Software - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6yi5


Chain - Source name: PDB / Chain - Initial model type: experimental model

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