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- EMDB-36358: The cryo-EM structure of 40-50 nm group Parvovirus from lamellae ... -

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Basic information

Entry
Database: EMDB / ID: EMD-36358
TitleThe cryo-EM structure of 40-50 nm group Parvovirus from lamellae surface milled by 8 keV Ga+ FIB at 3.54 Angstrom resolution.
Map dataCryoEM structure of 40-50 nm group parvovirus from lamellae surface milled by 8 keV Ga FIB. Block-based reconstruction.
Sample
  • Virus: Protoparvovirus
Keywordsicosahedral / VIRUS LIKE PARTICLE
Biological speciesProtoparvovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsYang Q / Zhang XZ
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930069 China
National Natural Science Foundation of China (NSFC)32150010 China
CitationJournal: Structure / Year: 2023
Title: The reduction of FIB damage on cryo-lamella by lowering energy of ion beam revealed by a quantitative analysis.
Authors: Qi Yang / Chunling Wu / Dongjie Zhu / Junxi Li / Jing Cheng / Xinzheng Zhang /
Abstract: Focused ion beam (FIB) is widely used for thinning frozen cells to produce lamellae for cryo-electron microscopy imaging and for protein structures study in vivo. However, FIB damages the lamellae ...Focused ion beam (FIB) is widely used for thinning frozen cells to produce lamellae for cryo-electron microscopy imaging and for protein structures study in vivo. However, FIB damages the lamellae and a quantitative experimental analysis of the damage is lacking. We used a 30-keV gallium FIB to prepare lamellae of a highly concentrated icosahedral virus sample. The viruses were grouped according to their distance from the surface of lamellae and reconstructed. Damage to the approximately 20-nm-thick outermost lamella surface was similar to that from exposure to 16 e/Å in a 300-kV cryo-electron microscope at high-resolution range. The damage was negligible at a depth beyond 50 nm, which was reduced to 30 nm if 8-keV Ga was used during polishing. We designed extra steps in the reconstruction refinement to maximize undamaged signals and increase the resolution. The results demonstrated that low-energy beam polishing was essential for high-quality thinner lamellae.
History
DepositionMay 30, 2023-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateOct 18, 2023-
Current statusOct 18, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36358.png

Downloads & links

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Map

FileDownload / File: emd_36358.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of 40-50 nm group parvovirus from lamellae surface milled by 8 keV Ga FIB. Block-based reconstruction.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 360 pix.
= 486. Å		1.35 Å/pix.
x 360 pix.
= 486. Å		1.35 Å/pix.
x 360 pix.
= 486. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0232
Minimum - Maximum-0.063505046 - 0.10274062
Average (Standard dev.)-0.00025111195 (±0.007350815)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 486.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 2 of 40-50 nm group parvovirus...

Fileemd_36358_half_map_1.map
AnnotationHalf map 2 of 40-50 nm group parvovirus from lamellae surface milled by 8 keV Ga FIB. Block-based reconstruction.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of 40-50 nm group parvovirus...

Fileemd_36358_half_map_2.map
AnnotationHalf map 1 of 40-50 nm group parvovirus from lamellae surface milled by 8 keV Ga FIB. Block-based reconstruction.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Protoparvovirus

EntireName: Protoparvovirus
Components
  • Virus: Protoparvovirus

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Supramolecule #1: Protoparvovirus

SupramoleculeName: Protoparvovirus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1506574 / Sci species name: Protoparvovirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 70 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Initial model generated by RELION.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Block-based reconstruction. / Number images used: 60000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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