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- EMDB-49574: Demo apoferritin data for Magellon -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-49574
TitleDemo apoferritin data for Magellon
Map data
Sample
  • Complex: Ferritin heavy chain, N-terminally processed
    • Protein or peptide: Mouse apoferritin heavy chain
KeywordsMETAL BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsStagg SM / Khoshbin B / Damodar P / Cianfrocco MA / Lander GC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143805 United States
CitationJournal: IUCrJ / Year: 2025
Title: Magellon - an extensible platform for cryo-EM data visualization, management and processing.
Authors: Behdad Khoshbin / Puneeth Damodar / Rupali R Garje / Frank H Schotanus / Nandagopal Nair / Lai Wei / Jan Hannes Schäfer / Gabriel C Lander / Michael A Cianfrocco / Scott M Stagg /
Abstract: Single-particle cryo-electron microscopy (cryo-EM) has revolutionized structural biology by enabling high-resolution determination of macromolecular structures. However, the field faces challenges in ...Single-particle cryo-electron microscopy (cryo-EM) has revolutionized structural biology by enabling high-resolution determination of macromolecular structures. However, the field faces challenges in data management, processing workflow integration and software extensibility. We present Magellon, an innovative cryo-EM software platform that addresses these challenges through a modern microservices architecture. Magellon consists of an extensible backend with a web based frontend that we call Magellon Viewer. Together, these combine high-performance computing capabilities with an intuitive user interface, enabling researchers to efficiently process and analyze cryo-EM data. The platform's distinguishing features include a plugin based architecture, distributed processing capabilities, comprehensive monitoring systems, and a novel approach to data organization and visualization. A key philosophy of the approach is that the Magellon backend provides a platform that uses robust industry-standard libraries to orchestrate computational tasks while offering users and developers flexibility in selecting the computational resources for performing calculations. Magellon represents a significant advancement in cryo-EM software infrastructure, offering flexibility, scalability and extensibility while maintaining ease of use.
History
DepositionMar 5, 2025-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49574.png

Downloads & links

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Map

FileDownload / File: emd_49574.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 256 pix.
= 202.212 Å		0.79 Å/pix.
x 256 pix.
= 202.212 Å		0.79 Å/pix.
x 256 pix.
= 202.212 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.78989 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0352
Minimum - Maximum-0.06443892 - 0.109959766
Average (Standard dev.)0.000024320665 (±0.009649201)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 202.21184 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_49574_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_49574_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ferritin heavy chain, N-terminally processed

EntireName: Ferritin heavy chain, N-terminally processed
Components
  • Complex: Ferritin heavy chain, N-terminally processed
    • Protein or peptide: Mouse apoferritin heavy chain

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Supramolecule #1: Ferritin heavy chain, N-terminally processed

SupramoleculeName: Ferritin heavy chain, N-terminally processed / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Mouse apoferritin heavy chain

MacromoleculeName: Mouse apoferritin heavy chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PSQVRQNYHQ DAEAAINRQI NLELYASYVY LSMSCYFDRD DVALKNFAKY FLHQSHEERE HAEKLMKLQN QRGGRIFLQD IKKPDRDDW ESGLNAMECA LHLEKSVNQS LLELHKLATD KNDPHLCDFI ETYYLSEQVK SIKELGDHVT NLRKMGAPEA G MAEYLFDK HTLG

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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 KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON APOLLO (4k x 4k) / Average electron dose: 60.0 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: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45802
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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