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- EMDB-70880: Apoferritin from mouse on graphene -

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Basic information

Entry
Database: EMDB / ID: EMD-70880
TitleApoferritin from mouse on graphene
Map data
Sample
  • Complex: Mouse ferritin heavy chain
    • Protein or peptide: Ferritin
KeywordsFerritin / METAL TRANSPORT
Function / homology
Function and homology information


Iron uptake and transport / Golgi Associated Vesicle Biogenesis / negative regulation of ferroptosis / ferroxidase / autolysosome / ferroxidase activity / Neutrophil degranulation / endocytic vesicle lumen / ferric iron binding / autophagosome ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / negative regulation of ferroptosis / ferroxidase / autolysosome / ferroxidase activity / Neutrophil degranulation / endocytic vesicle lumen / ferric iron binding / autophagosome / iron ion transport / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / mitochondrion / extracellular region / identical protein binding / membrane / cytosol
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Ferritin heavy chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsSchaefer JH / Lander GC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)R01 GM143805 United States
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2025
Title: CryoSift: an accessible and automated CNN-driven tool for cryo-EM 2D class selection.
Authors: Jan Hannes Schäfer / Austin Calza / Keegan Hom / Puneeth Damodar / Ruizhi Peng / Nebojša Bogdanović / Gabriel C Lander / Scott M Stagg / Michael A Cianfrocco /
Abstract: Single-particle cryo-electron microscopy (cryo-EM) has become an essential tool in structural biology. However, automating repetitive tasks remains an ongoing challenge in cryo-EM data-set processing. ...Single-particle cryo-electron microscopy (cryo-EM) has become an essential tool in structural biology. However, automating repetitive tasks remains an ongoing challenge in cryo-EM data-set processing. Here, we present a platform-independent convolutional neural network (CNN) tool for assessing the quality of 2D averages to enable the automatic selection of suitable particles for high-resolution reconstructions, termed CryoSift. We integrate CryoSift into a fully automated processing pipeline using the existing cryosparc-tools library. Our integrated and customizable 2D assessment workflow enables high-throughput processing that accommodates experienced to novice cryo-EM users.
History
DepositionMay 29, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70880.png

Downloads & links

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Map

FileDownload / File: emd_70880.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 320 pix.
= 236.8 Å		0.74 Å/pix.
x 320 pix.
= 236.8 Å		0.74 Å/pix.
x 320 pix.
= 236.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.41159463 - 0.7157678
Average (Standard dev.)-0.00006715101 (±0.03405738)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 236.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70880_msk_1.map
Projections & Slices
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Additional map: #1

Fileemd_70880_additional_1.map
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Half map: #1

Fileemd_70880_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_70880_half_map_2.map
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Sample components

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Entire : Mouse ferritin heavy chain

EntireName: Mouse ferritin heavy chain
Components
  • Complex: Mouse ferritin heavy chain
    • Protein or peptide: Ferritin

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Supramolecule #1: Mouse ferritin heavy chain

SupramoleculeName: Mouse ferritin heavy chain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Ferritin

MacromoleculeName: Ferritin / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTTASPSQVR QNYHQDAEAA INRQINLELY ASYVYLSMSC YFDRDDVALK NFAKYFLHQS HEEREHAEK LMKLQNQRGG RIFLQDIKKP DRDDWESGLN AMECALHLEK SVNQSLLELH K LATDKNDP HLCDFIETYY LSEQVKSIKE LGDHVTNLRK MGAPEAGMAE YLFDKHTLGH GD ES

UniProtKB: Ferritin heavy chain

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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 TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 119975
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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