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- EMDB-44745: 2.65 Angstrom Apoferritin single particle cryo-EM reconstruction ... -

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Basic information

Entry
Database: EMDB / ID: EMD-44745
Title2.65 Angstrom Apoferritin single particle cryo-EM reconstruction from a standard 120-keV LaB6 electron microscope (Tecnai G2 spirit) fitted with Gatan Alpine camera (a 100keV optimised direct electron detector).
Map dataB-Factor Sharpened Map
Sample
  • Complex: Apoferritin
KeywordsApoferritin / High resolution / LaB6 / Tecnai. / METAL TRANSPORT
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsVenugopal H / Ramm G
Funding support Australia, United States, 2 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)2010 Australia
Chan Zuckerberg InitiativeDAF2021-225399 United States
CitationJournal: Sci Adv / Year: 2025
Title: High-resolution cryo-EM using a common LaB 120-keV electron microscope equipped with a sub-200-keV direct electron detector.
Authors: Hariprasad Venugopal / Jesse Mobbs / Cyntia Taveneau / Daniel R Fox / Ziva Vuckovic / Sahil Gulati / Gavin Knott / Rhys Grinter / David Thal / Stephen Mick / Cory Czarnik / Georg Ramm /
Abstract: High-resolution cryo-electron microscopy (cryo-EM) requires costly 200- to 300-keV cryo-transmission electron microscopes (cryo-TEMs) with field emission gun (FEG) sources, stable columns, constant- ...High-resolution cryo-electron microscopy (cryo-EM) requires costly 200- to 300-keV cryo-transmission electron microscopes (cryo-TEMs) with field emission gun (FEG) sources, stable columns, constant-powered lenses, autoloader, and direct electron detectors (DED). Recent advances in 100-keV imaging with the emergence of sub-200-keV optimized DED technology promises the development of more affordable cryo-TEMs. So far, 100-keV imaging has required microscopes with FEG sources. We here explored whether a standard 120-keV TEMs with thermionic lanthanum hexaboride (LaB) source can be upgraded with a sub-200-keV DED for high-resolution cryo-EM. Using this imaging configuration, we successfully obtained a 2.65 Å reconstruction for apoferritin, 4.33 Å for 64-kDa hemoglobin, and 4.4 Å for an asymmetric 153kDa membrane protein GPCR. All results were achieved using standard automated data collection with SerialEM, demonstrating the feasibility to collect large cryo-EM datasets with a side-entry cryo-holder. These results showcase a widely accessible solution to obtaining interpretable cryo-EM structures at low cost and contribute to the "democratization" of cryo-EM.
History
DepositionMay 5, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44745.png

Downloads & links

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Map

FileDownload / File: emd_44745.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB-Factor Sharpened Map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 320 pix.
= 259.52 Å		0.81 Å/pix.
x 320 pix.
= 259.52 Å		0.81 Å/pix.
x 320 pix.
= 259.52 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.811 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.8316338 - 1.4461125
Average (Standard dev.)0.00014397153 (±0.076079816)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 259.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44745_msk_1.map
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Additional map: Raw Map

Fileemd_44745_additional_1.map
AnnotationRaw Map
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Half map: Half2

Fileemd_44745_half_map_1.map
AnnotationHalf2
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Half map: Half1

Fileemd_44745_half_map_2.map
AnnotationHalf1
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Sample components

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Entire : Apoferritin

EntireName: Apoferritin
Components
  • Complex: Apoferritin

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Supramolecule #1: Apoferritin

SupramoleculeName: Apoferritin / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 480 kDa/nm

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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: 8 / Details: 50 mM Tris-HCl (pH 8.0), 150 mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: GATAN ALPINE (2.3k x 3.2k) / Digitization - Dimensions - Width: 2304 pixel / Digitization - Dimensions - Height: 3240 pixel / Number grids imaged: 1 / Number real images: 923 / Average exposure time: 6.55 sec. / Average electron dose: 50.3 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 42000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Generated using ab-initio reconstruction routine in cryoSPARC
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.2.0) / Number images used: 127118
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.2.0)
FSC plot (resolution estimation)

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