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- EMDB-51779: Structure of apoferritin determined at 13K in 100 nm diameter holes. -

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Basic information

Entry
Database: EMDB / ID: EMD-51779
TitleStructure of apoferritin determined at 13K in 100 nm diameter holes.
Map data
Sample
  • Complex: Mouse heavy-chain apoferritin
KeywordsProtein Complex / METAL BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsDickerson JL / Naydenova K / Peet MJ / Wilson H / Nandy B / McMullan G / Morrison R / Crusso CJ
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_120117 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Reducing the effects of radiation damage in cryo-EM using liquid helium temperatures.
Authors: Joshua L Dickerson / Katerina Naydenova / Mathew J Peet / Hugh Wilson / Biplob Nandy / Greg McMullan / Robert Morrison / Christopher J Russo /
Abstract: The physical limit in determining the atomic structure of biological molecules is radiation damage. In electron cryomicroscopy, there have been numerous attempts to reduce the effects of radiation ...The physical limit in determining the atomic structure of biological molecules is radiation damage. In electron cryomicroscopy, there have been numerous attempts to reduce the effects of radiation damage by cooling the specimen beyond liquid-nitrogen temperatures, yet all failed to realize the potential improvement for single-particle structure determination. We have identified the physical causes of information loss at liquid-helium temperatures, and overcome them using a combination of nanoscale electron beam illumination and a gold specimen support with 100 nm diameter holes. This combination allowed structure determination where every frame in the exposure contained more information than was available with cryomicroscopy at liquid-nitrogen temperatures, matching expectations from crystal diffraction. Since a 100 nm hole is smaller than the field of view of a typical micrograph, the edges of the foil are directly visible in each micrograph. Protein molecules that are degraded tend to aggregate at the edges of foil holes and can constitute a significant fraction of the micrograph. This and the need for minimal water-foil irradiation will both be important to consider as new cryomicroscopes and specimen supports are developed for imaging molecules at extremely low temperatures where the effects of radiation damage are reduced.
History
DepositionOct 10, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51779.png

Downloads & links

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Map

FileDownload / File: emd_51779.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0124
Minimum - Maximum-0.022836065 - 0.0418111
Average (Standard dev.)0.00021807152 (±0.002549828)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51779_msk_1.map
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Half map: #2

Fileemd_51779_half_map_1.map
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Half map: #1

Fileemd_51779_half_map_2.map
Projections & Slices
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Sample components

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Entire : Mouse heavy-chain apoferritin

EntireName: Mouse heavy-chain apoferritin
Components
  • Complex: Mouse heavy-chain apoferritin

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Supramolecule #1: Mouse heavy-chain apoferritin

SupramoleculeName: Mouse heavy-chain apoferritin / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 13.0 K / Max: 13.0 K
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageCooling holder cryogen: HELIUM
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

11638

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1457
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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