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- EMDB-67082: Subtomogram average of Apoferrtin (11x11) using CRYO ARM 300II -

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Basic information

Entry
Database: EMDB / ID: EMD-67082
TitleSubtomogram average of Apoferrtin (11x11) using CRYO ARM 300II
Map data
Sample
  • Complex: Mouse apoferritin
    • Protein or peptide: Mouse apoferritin
KeywordsApoferrtin / RECOMBINATION
Function / homology
Function and homology information


Iron uptake and transport / Golgi Associated Vesicle Biogenesis / ferroxidase / negative regulation of ferroptosis / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation / ferric iron binding ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / ferroxidase / negative regulation of ferroptosis / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation / ferric iron binding / autophagosome / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / mitochondrion / extracellular region / membrane / identical protein binding / cytoplasm / 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 speciesEscherichia coli BL21(DE3) (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 2.04 Å
AuthorsYanagisawa H / Miyata T / Hosogi N / Kikkawa M / Namba K / Makino F
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP22am121003 Japan
Japan Agency for Medical Research and Development (AMED)JP17pc0101020 Japan
CitationJournal: AIMS Biophysics / Year: 2026
Title: Subtomogram averaging by cryo electron tomography using CRYO ARMTM 300 II for purified and cellular samples
Authors: Makino F / Yanagisawa H / Eisenstein F / Miyata T / Kinoshita M / Kikkawa M / Namba K
History
DepositionNov 14, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_67082.png

Downloads & links

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Map

FileDownload / File: emd_67082.map.gz / Format: CCP4 / Size: 56.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 246 pix.
= 248.46 Å		1.01 Å/pix.
x 246 pix.
= 248.46 Å		1.01 Å/pix.
x 246 pix.
= 248.46 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.01 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0046
Minimum - Maximum-0.014203375 - 0.022761432
Average (Standard dev.)-0.00000070948556 (±0.0010374982)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions246246246
Spacing246246246
CellA=B=C: 248.45999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67082_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67082_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_67082_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 : Mouse apoferritin

EntireName: Mouse apoferritin
Components
  • Complex: Mouse apoferritin
    • Protein or peptide: Mouse apoferritin

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Supramolecule #1: Mouse apoferritin

SupramoleculeName: Mouse apoferritin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: Mouse apoferritin

MacromoleculeName: Mouse apoferritin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString:
PSQVRQNYHQ DAEAAINRQI NLELYASYVY LSMSCYFDRD DVALKNFAKY FLHQSHEERE HAEKLMKLQN QRGGRIFLQD IKKPDRDDWE SGLNAMECAL HLEKSVNQSL LELHKLATDK NDPHLCDFIE TYYLSEQVKS IKELGDHVTN LRKMGAPEAG MAEYLFDKHT LG

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration4.0 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GOLD / Support film - #1 - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49505 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 50000

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Image processing

Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 154717
ExtractionNumber tomograms: 117 / Number images used: 158180 / Software: (Name: RELION (ver. 5), Warp)
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
FSC plot (resolution estimation)

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