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- EMDB-72123: Mouse apoferritin encapsulated in an MS2-nanocrate: MS2nc@ApoF -

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Basic information

Entry
Database: EMDB / ID: EMD-72123
TitleMouse apoferritin encapsulated in an MS2-nanocrate: MS2nc@ApoF
Map datasharpened map
Sample
  • Complex: Mouse apoferritin
KeywordsBacteriophage / VLP / MS2 / nanocrate / METAL BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.16 Å
AuthorsKopylov M / Bobe D / Jenkins MC / Zimanyi CM
Funding support United States, 3 items
OrganizationGrant numberCountry
Simons FoundationSF349247 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI148382 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA247484 United States
CitationJournal: Nat Methods / Year: 2026
Title: Overcoming air-water interface-induced artifacts in cryo-EM with protein nanocrates.
Authors: Matthew C Jenkins / Daija Bobe / Jake D Johnston / Jonah Cheung / Akira Karasawa / Christina M Zimanyi / Ömer Dermanci / Collin T McManus / M G Finn / Alex de Marco / Mykhailo Kopylov /
Abstract: Contact with the air-water interface can bias the orientation of macromolecules during cryo-electron microscopy sample preparation, leading to uneven sample distribution, preferred orientation and ...Contact with the air-water interface can bias the orientation of macromolecules during cryo-electron microscopy sample preparation, leading to uneven sample distribution, preferred orientation and damage to the molecules of interest. To prevent this, we describe a method to encapsulate target proteins within highly hydrophilic, structurally homogeneous and stable protein shells, which we refer to as 'nanocrates' for this purpose. Here we describe the packaging, data acquisition and reconstruction of three proof-of-principle examples, each illuminating a different aspect of the method: apoferritin (demonstrating high-resolution), thyroglobulin (solving a known preferred orientation problem) and 7,8-dihydroneopterin aldolase (a structure previously uncharacterized by cryo-electron microscopy).
History
DepositionAug 13, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72123.png

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Map

FileDownload / File: emd_72123.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 397.92 Å		0.83 Å/pix.
x 480 pix.
= 397.92 Å		0.83 Å/pix.
x 480 pix.
= 397.92 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.2140687 - 2.2936966
Average (Standard dev.)0.00033694645 (±0.080457054)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 397.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72123_msk_1.map
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Additional map: unsharpened map

Fileemd_72123_additional_1.map
Annotationunsharpened map
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Half map: #1

Fileemd_72123_half_map_1.map
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Half map: #2

Fileemd_72123_half_map_2.map
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Sample components

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Entire : Mouse apoferritin

EntireName: Mouse apoferritin
Components
  • Complex: Mouse apoferritin

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Supramolecule #1: Mouse apoferritin

SupramoleculeName: Mouse apoferritin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Ferritin heavy chain
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 stateparticle

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Sample preparation

Concentration8 mg/mL
BufferpH: 8.5 / Details: 100 mM Tris-HCl [pH 8.5], 80 mM KCl, 10 mM MgCl2
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 2860 / Average exposure time: 1.25 sec. / Average electron dose: 54.58 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000
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

Particle selectionNumber selected: 348343
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 69418
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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