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- EMDB-35916: Cryo-EPty SPA at CSA of 3.26 mrad -

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Basic information

Entry
Database: EMDB / ID: EMD-35916
TitleCryo-EPty SPA at CSA of 3.26 mrad
Map data
Sample
  • Virus: Rotavirus A
KeywordsComplex / VIRUS
Biological speciesRotavirus A
Methodsingle particle reconstruction / cryo EM / Resolution: 32.9 Å
AuthorsPei XD / Wang P
Funding support China, United Kingdom, European Union, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)11874199 China
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
Wellcome Trust206422/Z/17/Z United Kingdom
European Research Council (ERC)101021133European Union
CitationJournal: Nat Commun / Year: 2023
Title: Cryogenic electron ptychographic single particle analysis with wide bandwidth information transfer.
Authors: Xudong Pei / Liqi Zhou / Chen Huang / Mark Boyce / Judy S Kim / Emanuela Liberti / Yiming Hu / Takeo Sasaki / Peter D Nellist / Peijun Zhang / David I Stuart / Angus I Kirkland / Peng Wang /
Abstract: Advances in cryogenic transmission electron microscopy have revolutionised the determination of many macromolecular structures at atomic or near-atomic resolution. This method is based on ...Advances in cryogenic transmission electron microscopy have revolutionised the determination of many macromolecular structures at atomic or near-atomic resolution. This method is based on conventional defocused phase contrast imaging. However, it has limitations of weaker contrast for small biological molecules embedded in vitreous ice, in comparison with cryo-ptychography, which shows increased contrast. Here we report a single-particle analysis based on the use of ptychographic reconstruction data, demonstrating that three dimensional reconstructions with a wide information transfer bandwidth can be recovered by Fourier domain synthesis. Our work suggests future applications in otherwise challenging single particle analyses, including small macromolecules and heterogeneous or flexible particles. In addition structure determination in situ within cells without the requirement for protein purification and expression may be possible.
History
DepositionApr 12, 2023-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateJun 14, 2023-
Current statusJun 14, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35916.png

Downloads & links

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Map

FileDownload / File: emd_35916.map.gz / Format: CCP4 / Size: 58.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
4.65 Å/pix.
x 248 pix.
= 1153.16 Å		4.65 Å/pix.
x 248 pix.
= 1153.16 Å		4.65 Å/pix.
x 248 pix.
= 1153.16 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.64984 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.564
Minimum - Maximum0.0 - 1.0
Average (Standard dev.)0.47370514 (±0.039501335)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions248248248
Spacing248248248
CellA=B=C: 1153.1603 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35916_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35916_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rotavirus A

EntireName: Rotavirus A
Components
  • Virus: Rotavirus A

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Supramolecule #1: Rotavirus A

SupramoleculeName: Rotavirus A / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 28875 / Sci species name: Rotavirus A / Sci species strain: SA 11 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / Name: Double layered particles / Diameter: 720.0 Å

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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

Concentration8 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: OTHER / Average electron dose: 24.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 4.0 µm
Sample stageSpecimen holder model: GATAN ELSA 698 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER

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Image processing

Particle selectionNumber selected: 443
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 32.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 106
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Avg.num./class: 80 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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