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- EMDB-14767: Mouse heavy chain apoferritin in plunge-frozen vitrified ice -

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Basic information

Entry
Database: EMDB / ID: EMD-14767
TitleMouse heavy chain apoferritin in plunge-frozen vitrified ice
Map data
Sample
  • Complex: Mouse heavy chain apoferritin in plunge-frozen vitrified ice
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.57 Å
AuthorsHarder OF / Voss JM / Olshin PK / Drabbels M / Lorenz UJ
Funding supportEuropean Union, Switzerland, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)759145European Union
Swiss National Science FoundationPP00P2_163681 Switzerland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Microsecond melting and revitrification of cryo samples: protein structure and beam-induced motion.
Authors: Oliver F Harder / Jonathan M Voss / Pavel K Olshin / Marcel Drabbels / Ulrich J Lorenz /
Abstract: A novel approach to time-resolved cryo-electron microscopy (cryo-EM) has recently been introduced that involves melting a cryo sample with a laser beam to allow protein dynamics to briefly occur in ...A novel approach to time-resolved cryo-electron microscopy (cryo-EM) has recently been introduced that involves melting a cryo sample with a laser beam to allow protein dynamics to briefly occur in the liquid, before trapping the particles in their transient configurations by rapidly revitrifying the sample. With a time resolution of just a few microseconds, this approach is notably fast enough to study the domain motions that are typically associated with the activity of proteins but which have previously remained inaccessible. Here, crucial details are added to the characterization of the method. It is shown that single-particle reconstructions of apoferritin and Cowpea chlorotic mottle virus from revitrified samples are indistinguishable from those from conventional samples, demonstrating that melting and revitrification leaves the particles intact and that they do not undergo structural changes within the spatial resolution afforded by the instrument. How rapid revitrification affects the properties of the ice is also characterized, showing that revitrified samples exhibit comparable amounts of beam-induced motion. The results pave the way for microsecond time-resolved studies of the conformational dynamics of proteins and open up new avenues to study the vitrification process and to address beam-induced specimen movement.
History
DepositionApr 13, 2022-
Header (metadata) releaseJul 13, 2022-
Map releaseJul 13, 2022-
UpdateJul 13, 2022-
Current statusJul 13, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_14767.map.gz / Format: CCP4 / Size: 30.5 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.)
0.98 Å/pix.
x 200 pix.
= 195. Å
0.98 Å/pix.
x 200 pix.
= 195. Å
0.98 Å/pix.
x 200 pix.
= 195. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.975 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.3020291 - 0.62218386
Average (Standard dev.)0.008474695 (±0.057066076)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 195.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_14767_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_14767_half_map_2.map
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Sample components

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Entire : Mouse heavy chain apoferritin in plunge-frozen vitrified ice

EntireName: Mouse heavy chain apoferritin in plunge-frozen vitrified ice
Components
  • Complex: Mouse heavy chain apoferritin in plunge-frozen vitrified ice

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Supramolecule #1: Mouse heavy chain apoferritin in plunge-frozen vitrified ice

SupramoleculeName: Mouse heavy chain apoferritin in plunge-frozen vitrified ice
type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

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Electron microscopy

MicroscopeJEOL 2200FS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49885
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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