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- EMDB-54082: 1.8 A structure of SiO2-sealed and revitrified (210 us) mouse hea... -

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Basic information

Entry
Database: EMDB / ID: EMD-54082
Title1.8 A structure of SiO2-sealed and revitrified (210 us) mouse heavy chain Apoferritin
Map dataEM map for Apoferritin - sealed and revitrified
Sample
  • Complex: Mouse heavy-chain Apoferritin
Keywordsapoferritin / METAL BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.8 Å
AuthorsCurtis WA / Hruby J / Krueger CR / Barrass SV / Drabbels M / Lorenz UJ
Funding support Switzerland, United States, 2 items
OrganizationGrant numberCountry
Swiss National Science FoundationTMCG-2_213773 Switzerland
National Institutes of Health/National Center for Research Resources (NIH/NCRR)U54AI170752 United States
CitationJournal: To Be Published
Title: Ultrathin Liquid Cells for Microsecond Time-Resolved Cryo-EM
Authors: Curtis WA / Hruby J / Krueger CR / Barrass SV / Drabbels M / Lorenz UJ
History
DepositionJun 19, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54082.png

Downloads & links

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Map

FileDownload / File: emd_54082.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map for Apoferritin - sealed and revitrified
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 440 pix.
= 322.08 Å		0.73 Å/pix.
x 440 pix.
= 322.08 Å		0.73 Å/pix.
x 440 pix.
= 322.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.732 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0349
Minimum - Maximum-0.13081023 - 0.50100714
Average (Standard dev.)0.001150291 (±0.017819205)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 322.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map B for Apoferritin - sealed and revitrified

Fileemd_54082_half_map_1.map
AnnotationHalf-map B for Apoferritin - sealed and revitrified
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B for Apoferritin - sealed and revitrified

Fileemd_54082_half_map_2.map
AnnotationHalf-map B for Apoferritin - sealed and revitrified
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 heavy-chain Apoferritin

EntireName: Mouse heavy-chain Apoferritin
Components
  • Complex: Mouse heavy-chain Apoferritin

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Supramolecule #1: Mouse heavy-chain Apoferritin

SupramoleculeName: Mouse heavy-chain Apoferritin / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

Concentration8 mg/mL
BufferpH: 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 170473
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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