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- EMDB-73641: The Kaggle CryoET Object Identification Challenge: first place be... -

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Basic information

Entry
Database: EMDB / ID: EMD-73641
TitleThe Kaggle CryoET Object Identification Challenge: first place beta-amylase
Map datamain map
Sample
  • Organelle or cellular component: HEK293T cell lysate mixed with purified proteins on functionalized EM grids
Keywordsbeta-amylase / HYDROLASE
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 10.6 Å
AuthorsPeck A / Hutchings J / Schwartz J / Paraan M
Funding support United States, 1 items
OrganizationGrant numberCountry
Chan Zuckerberg InitiativeCZII2023327779 United States
CitationJournal: Nat Methods / Year: 2025
Title: A realistic phantom dataset for benchmarking cryo-ET data annotation.
Authors: Ariana Peck / Yue Yu / Jonathan Schwartz / Anchi Cheng / Utz Heinrich Ermel / Joshua Hutchings / Saugat Kandel / Dari Kimanius / Elizabeth A Montabana / Daniel Serwas / Hannah Siems / Feng ...Authors: Ariana Peck / Yue Yu / Jonathan Schwartz / Anchi Cheng / Utz Heinrich Ermel / Joshua Hutchings / Saugat Kandel / Dari Kimanius / Elizabeth A Montabana / Daniel Serwas / Hannah Siems / Feng Wang / Zhuowen Zhao / Shawn Zheng / Matthias Haury / David A Agard / Clinton S Potter / Bridget Carragher / Kyle Harrington / Mohammadreza Paraan /
Abstract: Cryo-electron tomography (cryo-ET) is a powerful technique for imaging molecular complexes in their native cellular environments. However, identifying the vast majority of molecular species in ...Cryo-electron tomography (cryo-ET) is a powerful technique for imaging molecular complexes in their native cellular environments. However, identifying the vast majority of molecular species in cellular tomograms remains prohibitively difficult. Machine learning (ML) methods provide an opportunity to automate the annotation process, but algorithm development has been hindered by the lack of large, standardized datasets. Here we present an experimental phantom dataset with comprehensive ground-truth annotations for six molecular species to spur new algorithm development and benchmark existing tools. This annotated dataset is available on the CryoET Data Portal with infrastructure to streamline access for methods developers across fields.
History
DepositionOct 29, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73641.png

Downloads & links

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Map

FileDownload / File: emd_73641.map.gz / Format: CCP4 / Size: 2.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
3.02 Å/pix.
x 84 pix.
= 253.68 Å		3.02 Å/pix.
x 84 pix.
= 253.68 Å		3.02 Å/pix.
x 84 pix.
= 253.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0076
Minimum - Maximum-0.0042385287 - 0.016640142
Average (Standard dev.)0.00018634505 (±0.0015120138)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions848484
Spacing848484
CellA=B=C: 253.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73641_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map from refinement

Fileemd_73641_half_map_1.map
Annotationhalf-map from refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map from refinement

Fileemd_73641_half_map_2.map
Annotationhalf-map from refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HEK293T cell lysate mixed with purified proteins on functionalize...

EntireName: HEK293T cell lysate mixed with purified proteins on functionalized EM grids
Components
  • Organelle or cellular component: HEK293T cell lysate mixed with purified proteins on functionalized EM grids

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Supramolecule #1: HEK293T cell lysate mixed with purified proteins on functionalize...

SupramoleculeName: HEK293T cell lysate mixed with purified proteins on functionalized EM grids
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293T

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 10.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5)
Details: Initial low-resolution alignment against the same model. All subsequent high-resolution refinements are independent.
Number subtomograms used: 970
ExtractionNumber tomograms: 328 / Number images used: 970 / Software - Name: RELION (ver. 5)
CTF correctionSoftware - Name: RELION (ver. 5) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
FSC plot (resolution estimation)

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