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- EMDB-40267: CryoEM map of a T=1 off-target state of design Ico(T=4)-4 -

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Basic information

Entry
Database: EMDB / ID: EMD-40267
TitleCryoEM map of a T=1 off-target state of design Ico(T=4)-4
Map datasharpened map from deepEMhancer
Sample
  • Complex: Icos(T=4)-4
Keywordsicosahedral nanocage / T=4 / T=4 icosahedra / T=1 / T=1 icosahedra / off-target / nanomaterial / computational design / de novo / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.54 Å
AuthorsBorst AJ / Kibler RD / Lee S
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2025
Title: Four-component protein nanocages designed by programmed symmetry breaking.
Authors: Sangmin Lee / Ryan D Kibler / Green Ahn / Yang Hsia / Andrew J Borst / Annika Philomin / Madison A Kennedy / Buwei Huang / Barry Stoddard / David Baker /
Abstract: Four, eight or twenty C3 symmetric protein trimers can be arranged with tetrahedral, octahedral or icosahedral point group symmetry to generate closed cage-like structures. Viruses access more ...Four, eight or twenty C3 symmetric protein trimers can be arranged with tetrahedral, octahedral or icosahedral point group symmetry to generate closed cage-like structures. Viruses access more complex higher triangulation number icosahedral architectures by breaking perfect point group symmetry, but nature appears not to have explored similar symmetry breaking for tetrahedral or octahedral symmetries. Here we describe a general design strategy for building higher triangulation number architectures starting from regular polyhedra through pseudosymmetrization of trimeric building blocks. Electron microscopy confirms the structures of T = 4 cages with 48 (tetrahedral), 96 (octahedral) and 240 (icosahedral) subunits, each with 4 distinct chains and 6 different protein-protein interfaces, and diameters of 33 nm, 43 nm and 75 nm, respectively. Higher triangulation number viruses possess very sophisticated functionalities; our general route to higher triangulation number nanocages should similarly enable a next generation of multiple antigen-displaying vaccine candidates and targeted delivery vehicles.
History
DepositionMar 31, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40267.png

Downloads & links

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Map

FileDownload / File: emd_40267.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map from deepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.56 Å/pix.
x 360 pix.
= 920.52 Å		2.56 Å/pix.
x 360 pix.
= 920.52 Å		2.56 Å/pix.
x 360 pix.
= 920.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.557 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.226
Minimum - Maximum-0.0001407214 - 1.3843389
Average (Standard dev.)0.0010108374 (±0.021511747)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 920.51996 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map from final Non-Uniform Refinement

Fileemd_40267_additional_1.map
Annotationunsharpened map from final Non-Uniform Refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A from final Non-Uniform Refinement

Fileemd_40267_half_map_1.map
Annotationhalf map A from final Non-Uniform Refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B from final Non-Uniform Refinement

Fileemd_40267_half_map_2.map
Annotationhalf map B from final Non-Uniform Refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Icos(T=4)-4

EntireName: Icos(T=4)-4
Components
  • Complex: Icos(T=4)-4

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Supramolecule #1: Icos(T=4)-4

SupramoleculeName: Icos(T=4)-4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / Details: A hierarchically designed T=4 icosahedral nanocage
Source (natural)Organism: synthetic construct (others)

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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: 8 / Details: 25mM Tris, 300mM NaCl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 6678 / Average electron dose: 61.463 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1172
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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