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- EMDB-13769: CryoEM structure of Apoferritin at 2.6A from Tundra, 100kV microscope -

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Basic information

Entry
Database: EMDB / ID: EMD-13769
TitleCryoEM structure of Apoferritin at 2.6A from Tundra, 100kV microscope
Map dataApoferritin data from Tundra, 100kV microscope with CetaF detector
Sample
  • Complex: Apoferritin
KeywordsFe / METAL BINDING PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsKaria D / Hlavenkova H / Koh A / Malinsky M / Yu L / Kotecha A
Funding support1 items
OrganizationGrant numberCountry
Other privatexxxxx
CitationJournal: Structure / Year: 2025
Title: Sub-3 Å resolution protein structure determination by single-particle cryo-EM at 100 keV.
Authors: Dimple Karia / Adrian F Koh / Wen Yang / Victoria I Cushing / Benjamin Basanta / Daniel B Mihaylov / Sagar Khavnekar / Ondřej Vyroubal / Miloš Malínský / Ondřej Sháněl / Vojtěch ...Authors: Dimple Karia / Adrian F Koh / Wen Yang / Victoria I Cushing / Benjamin Basanta / Daniel B Mihaylov / Sagar Khavnekar / Ondřej Vyroubal / Miloš Malínský / Ondřej Sháněl / Vojtěch Doležal / Jürgen Plitzko / Lingbo Yu / Gabriel C Lander / A Radu Aricescu / Basil J Greber / Abhay Kotecha /
Abstract: Cryoelectron microscopy (cryo-EM) has transformed structural biology by providing high-resolution insights into biological macromolecules. We report sub-3 Å resolution structures using the 100 keV ...Cryoelectron microscopy (cryo-EM) has transformed structural biology by providing high-resolution insights into biological macromolecules. We report sub-3 Å resolution structures using the 100 keV Tundra cryo-TEM, equipped with the Falcon C direct electron detector (DED). This system combines advanced optics, extreme-brightness field emission gun (XFEG), and SP-TWIN lens to enhance coherence and resolution. The semi-automated loader reduced contamination and drift, enabling extended data collection, while the high detective quantum efficiency (DQE) of Falcon C improved signal-to-noise ratio. We validated performance by determining structures of biological samples, including apoferritin (2.1 Å), T20S proteasome (2.7 Å), GABA receptor (2.8 Å), hemoglobin (5.0 Å), transthyretin (3.5 Å), and AAV9 capsid (2.8 Å), spanning 50 kDa-3.9 MDa. This work highlights the potential of 100 keV transmission electron microscopes (TEMs) to make cryo-EM more accessible. It sets a precedent for using lower voltage TEMs not only for screening, but also for high-resolution protein structure determination.
History
DepositionOct 21, 2021-
Header (metadata) releaseJan 26, 2022-
Map releaseJan 26, 2022-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.13
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13769.png

Downloads & links

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Map

FileDownload / File: emd_13769.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationApoferritin data from Tundra, 100kV microscope with CetaF detector
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 256 pix.
= 268.186 Å		1.05 Å/pix.
x 256 pix.
= 268.186 Å		1.05 Å/pix.
x 256 pix.
= 268.186 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0476 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13 / Movie #1: 0.13
Minimum - Maximum-0.356153 - 0.556499
Average (Standard dev.)0.00026428947 (±0.02573985)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 268.1856 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.04760156251.04760156251.0476015625
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z268.186268.186268.186
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.3560.5560.000

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Supplemental data

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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: Escherichia coli (E. coli)
Molecular weightTheoretical: 480 KDa

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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

Concentration4 mg/mL
BufferpH: 7.5 / Details: 20mM HEPES pH 7.5 and 300mM NaCl
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details4mg/ml protein in 20mM HEPES pH 7.5 and 300mM NaCl

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Electron microscopy

MicroscopeTFS TUNDRA
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Number grids imaged: 1 / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.6 mm / Nominal magnification: 180000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 413168
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 165082
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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