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- EMDB-65822: Apoferritin (118% Super resolution Nyquist, 236% physical Nyquist... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-65822
TitleApoferritin (118% Super resolution Nyquist, 236% physical Nyquist) by PASR on Acquisition-time Super Resolution K3 data
Map dataPASR-on-ASR apoferritin masked map
Sample
  • Complex: Apoferritin (PASR-on-ASR)
    • Protein or peptide: Ferritin heavy chain, N-terminally processed
  • Ligand: FE (III) ION
KeywordsApoferritin / iron binding / PASR / METAL BINDING PROTEIN
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: 1.67 Å
AuthorsBurton-Smith RN / Murata K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Post Acquisition Super Resolution for Cryo-Electron Microscopy
Authors: Burton-Smith RN / Murata K
History
DepositionAug 12, 2025-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65822.png

Downloads & links

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Map

FileDownload / File: emd_65822.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPASR-on-ASR apoferritin masked map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.49 Å/pix.
x 440 pix.
= 216.788 Å		0.49 Å/pix.
x 440 pix.
= 216.788 Å		0.49 Å/pix.
x 440 pix.
= 216.788 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.4927 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0453
Minimum - Maximum-0.1535111 - 0.31416026
Average (Standard dev.)0.000023506673 (±0.0113285845)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 216.78801 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: PASR-on-ASR apoferritin sharpened map

Fileemd_65822_additional_1.map
AnnotationPASR-on-ASR apoferritin sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PASR-on-ASR apoferritin half map 1

Fileemd_65822_half_map_1.map
AnnotationPASR-on-ASR apoferritin half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PASR-on-ASR apoferritin half map 2

Fileemd_65822_half_map_2.map
AnnotationPASR-on-ASR apoferritin half map 2
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 (PASR-on-ASR)

EntireName: Apoferritin (PASR-on-ASR)
Components
  • Complex: Apoferritin (PASR-on-ASR)
    • Protein or peptide: Ferritin heavy chain, N-terminally processed
  • Ligand: FE (III) ION

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Supramolecule #1: Apoferritin (PASR-on-ASR)

SupramoleculeName: Apoferritin (PASR-on-ASR) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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

MacromoleculeName: Ferritin heavy chain, N-terminally processed / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 20.304818 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SPSQVRQNYH QDAEAAINRQ INLELYASYV YLSMSCYFDR DDVALKNFAK YFLHQSHEER EHAEKLMKLQ NQRGGRIFLQ DIKKPDRDD WESGLNAMEC ALHLEKSVNQ SLLELHKLAT DKNDPHLCDF IETYYLSEQV KSIKELGDHV TNLRKMGAPE A GMAEYLFD KHTLGH

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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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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: 1.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 2910547
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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