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- EMDB-40268: CryoEM map of a de novo designed T=4 octahedral nanocage hierarch... -

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Basic information

Entry
Database: EMDB / ID: EMD-40268
TitleCryoEM map of a de novo designed T=4 octahedral nanocage hierarchically built from pseudosymmetric trimers; design Oct(T=4)-3
Map datasharpened map using DeepEMhancer
Sample
  • Complex: Oct(T=4)-3
    • Protein or peptide: Oct(T=4)-3 chain A
    • Protein or peptide: Oct(T=4)-3 chain B
    • Protein or peptide: Oct(T=4)-3 chain C
    • Protein or peptide: Oct(T=4)-3 chain ho
Keywordsicosahedral nanocage / T=4 / T=4 icosahedra / nanomaterial / computational design / de novo / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.87 Å
AuthorsPhilomin A / Borst AJ / Kibler RD
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_40268.png

Downloads & links

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Map

FileDownload / File: emd_40268.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map using DeepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.36 Å/pix.
x 300 pix.
= 708. Å		2.36 Å/pix.
x 300 pix.
= 708. Å		2.36 Å/pix.
x 300 pix.
= 708. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.103
Minimum - Maximum-0.0017326495 - 1.6085112
Average (Standard dev.)0.0021726172 (±0.028964581)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 707.99994 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_40268_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_40268_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_40268_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 : Oct(T=4)-3

EntireName: Oct(T=4)-3
Components
  • Complex: Oct(T=4)-3
    • Protein or peptide: Oct(T=4)-3 chain A
    • Protein or peptide: Oct(T=4)-3 chain B
    • Protein or peptide: Oct(T=4)-3 chain C
    • Protein or peptide: Oct(T=4)-3 chain ho

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Supramolecule #1: Oct(T=4)-3

SupramoleculeName: Oct(T=4)-3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: A hierarchically designed T=4 octahedral nanocage
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Oct(T=4)-3 chain A

MacromoleculeName: Oct(T=4)-3 chain A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSLELALKA LQILVNAAYV LAEIARDRGN EELLEKAARL AEEAARQAER IARQARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEL LEYAARLAEE AARQAIEIWA QAMEEGNQQL RTKAAHIILR AAEVLLEIAR DRGNQELLEK AASLVDAVAA LQQAAAAILE ...String:
MGSLELALKA LQILVNAAYV LAEIARDRGN EELLEKAARL AEEAARQAER IARQARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEL LEYAARLAEE AARQAIEIWA QAMEEGNQQL RTKAAHIILR AAEVLLEIAR DRGNQELLEK AASLVDAVAA LQQAAAAILE GDVEKAVRAA QEAVKAAKEA GDNDMLRAVA IAALRIAKEA EKQGNVEVAV KAARVAVEAA KQAGDQDVLL KVATQAARIA LEAIKQGNLE VKLEALKVAQ EALKQTGGSG GSHHHHHH

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Macromolecule #2: Oct(T=4)-3 chain B

MacromoleculeName: Oct(T=4)-3 chain B / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
SequenceString: MGSPRLVLRA LENMVRAAHT LAEIARDNGN EEWLERAARL AEEVARRAER LAREARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEE LEYAARLAEE AARQAIEIAA QAMEEGNLEL ALKALQIIVN AAYVLAEIAR DRGNEELLEK AASLAEAAAA LAEAIAAILE ...String:
MGSPRLVLRA LENMVRAAHT LAEIARDNGN EEWLERAARL AEEVARRAER LAREARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEE LEYAARLAEE AARQAIEIAA QAMEEGNLEL ALKALQIIVN AAYVLAEIAR DRGNEELLEK AASLAEAAAA LAEAIAAILE GDVEKAVRAA QEAVKAAKEA GDNDMLRAVA IAALRIAKEA EKQGNVEVAV KAARVAVEAA KQAGDQDVLK KVAAQAARIM LEAIKQGNTE VALEALKVAQ EALKQTGGSG GSHHHHHH

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Macromolecule #3: Oct(T=4)-3 chain C

MacromoleculeName: Oct(T=4)-3 chain C / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSPELFLQD LRSLVEAARI LARLARQRGD EHALERAARW AEQAARQAER LARQARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEL LEYAARLAEE AARQAIEIAA QAMEEGNFEL ALEALEIINE AARVLARIAH HRGNQELLEK AASLTHASAA LSRAIAAILE ...String:
MGSPELFLQD LRSLVEAARI LARLARQRGD EHALERAARW AEQAARQAER LARQARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEL LEYAARLAEE AARQAIEIAA QAMEEGNFEL ALEALEIINE AARVLARIAH HRGNQELLEK AASLTHASAA LSRAIAAILE GDVEKAVRAA QEAVKAAKEA GDNDMLRAVA IAALRIAKEA EKQGNVEVAV KAARVAVEAA KQAGDNDVLR KVAEQALRIA KEAEKQGNVI VAMKAIDVAV EAAGQAGDID VIKKVADQTQ RIVDEWLKQG

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Macromolecule #4: Oct(T=4)-3 chain ho

MacromoleculeName: Oct(T=4)-3 chain ho / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSPELFLQD LRSLVEAARI LARLARQRGD EHALERAARW AEQAARQAER LARQARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEL LEYAARLAEE AARQAIEIWA QAMEEGNQQL RTKAAHIILR AAEVLLEIAR DRGNQELLEK AASLVDAVAA LQQAAAAILE ...String:
MGSPELFLQD LRSLVEAARI LARLARQRGD EHALERAARW AEQAARQAER LARQARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEL LEYAARLAEE AARQAIEIWA QAMEEGNQQL RTKAAHIILR AAEVLLEIAR DRGNQELLEK AASLVDAVAA LQQAAAAILE GDVEKAVRAA QEAVKAAKEA GDNDMLRAVA IAALRIAKEA EKQGNVEVAV KAARVAVEAA KQAGDNDVLR KVAEQALRIA KEAEKQGNVY VAAKAVQVAA EAAKQAGDID VLKKVIGQTQ RIRDEWVKQG GSGGSHHHHH H

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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

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing

Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29069
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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