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- EMDB-41619: Cryo-EM structure of Apoferritin collected by SerialEM on Glacios... -

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Basic information

Entry
Database: EMDB / ID: EMD-41619
TitleCryo-EM structure of Apoferritin collected by SerialEM on Glacios at 2.1 Angstrom resolution
Map data
Sample
  • Cell: Apoferritin
    • Protein or peptide: Ferritin heavy chain
  • Ligand: FE (III) ION
  • Ligand: ZINC ION
KeywordsApoferritin / Glacios / Falcon4 / Selectris energy filter / benchmark / METAL BINDING PROTEIN
Function / homology
Function and homology information


Iron uptake and transport / Golgi Associated Vesicle Biogenesis / iron ion sequestering activity / negative regulation of ferroptosis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / Neutrophil degranulation / endocytic vesicle lumen ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / iron ion sequestering activity / negative regulation of ferroptosis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / Neutrophil degranulation / endocytic vesicle lumen / ferric iron binding / autophagosome / ferrous iron binding / 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
AuthorsJia L / Ruben EA / Olsen SK / Wasmuth EV
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of Apoferritin collected by SerialEM on Glacios at 2.1 Angstrom resolution
Authors: Jia L / Ruben EA / Olsen SK / Wasmuth EV
History
DepositionAug 15, 2023-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41619.png

Downloads & links

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Map

FileDownload / File: emd_41619.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 320 pix.
= 278.4 Å		0.87 Å/pix.
x 320 pix.
= 278.4 Å		0.87 Å/pix.
x 320 pix.
= 278.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.323
Minimum - Maximum-1.3402083 - 2.1882904
Average (Standard dev.)0.000072986484 (±0.10076378)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 278.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41619_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41619_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41619_half_map_2.map
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
  • Cell: Apoferritin
    • Protein or peptide: Ferritin heavy chain
  • Ligand: FE (III) ION
  • Ligand: ZINC ION

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Supramolecule #1: Apoferritin

SupramoleculeName: Apoferritin / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Ferritin heavy chain

MacromoleculeName: Ferritin heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: ferroxidase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 21.097631 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTTASPSQVR QNYHQDAEAA INRQINLELY ASYVYLSMSC YFDRDDVALK NFAKYFLHQS HEEREHAEKL MKLQNQRGGR IFLQDIKKP DRDDWESGLN AMECALHLEK SVNQSLLELH KLATDKNDPH LCDFIETYYL SEQVKSIKEL GDHVTNLRKM G APEAGMAE YLFDKHTLGH GDES

UniProtKB: Ferritin heavy chain

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Macromolecule #2: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 24 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 54.0 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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6sht

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 261652
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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