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- EMDB-19880: Cryo-EM structure of human apoferritin (grid prepared with EasyGr... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-19880
TitleCryo-EM structure of human apoferritin (grid prepared with EasyGrid technology)
Map dataApoferritin map processed in cryoSPARC from 188570 particles (4200 micrographs). Map automatically sharpened in cryoSPARC.
Sample
  • Complex: Apoferritin
Keywordsapoferritin / OXIDOREDUCTASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.94 Å
AuthorsGemin O / Mattei S / Papp G
Funding support Germany, 1 items
OrganizationGrant numberCountry
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND Germany
CitationJournal: bioRxiv / Year: 2024
Title: EasyGrid: a versatile platform for automated cryo-EM sample preparation and quality control
Authors: Gemin O / Armijo V / Hons M / Bissardon C / Linares R / Bowler MW / Wolff G / Kovalev K / Babenko A / Salo VT / Schneider S / Rossi C / Lecomte L / Deckers T / Lauzier K / Janocha R / ...Authors: Gemin O / Armijo V / Hons M / Bissardon C / Linares R / Bowler MW / Wolff G / Kovalev K / Babenko A / Salo VT / Schneider S / Rossi C / Lecomte L / Deckers T / Lauzier K / Janocha R / Felisaz F / Sinoir J / Galej W / Mahamid J / Mueller CW / Eustermann S / Mattei S / Cipriani F / Papp G
History
DepositionMar 18, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19880.png

Downloads & links

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Map

FileDownload / File: emd_19880.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationApoferritin map processed in cryoSPARC from 188570 particles (4200 micrographs). Map automatically sharpened in cryoSPARC.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 360 pix.
= 263.16 Å		0.73 Å/pix.
x 360 pix.
= 263.16 Å		0.73 Å/pix.
x 360 pix.
= 263.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.731 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.14
Minimum - Maximum-3.4698966 - 5.8951526
Average (Standard dev.)0.0051895636 (±0.20132075)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 263.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19880_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Apoferritin map processed in cryoSPARC from 188570 particles...

Fileemd_19880_additional_1.map
AnnotationApoferritin map processed in cryoSPARC from 188570 particles (4200 micrographs). Full map (not sharpened).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Apoferritin map processed in cryoSPARC from 188570 particles...

Fileemd_19880_half_map_1.map
AnnotationApoferritin map processed in cryoSPARC from 188570 particles (4200 micrographs). Half-map #2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Apoferritin map processed in cryoSPARC from 188570 particles...

Fileemd_19880_half_map_2.map
AnnotationApoferritin map processed in cryoSPARC from 188570 particles (4200 micrographs). Half-map #1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: Homo sapiens (human)

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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 TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 655884
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 188570
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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