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- EMDB-70792: Designed one-component T=3 quasisymmetric protein nanocage pentam... -

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Basic information

Entry
Database: EMDB / ID: EMD-70792
TitleDesigned one-component T=3 quasisymmetric protein nanocage pentamer sub-particle region
Map dataEM focused refinement map
Sample
  • Complex: SLQ21
Keywordsnanoparticle / quasisymmetry / de novo design / DE NOVO PROTEIN
Biological speciesE coli (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsLee S / Chmielewski D / Wang S / Kibler R / Park YJ / Veesler D / Baker D
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2026
Title: Design of one-component quasisymmetric protein nanocages.
Authors: Sangmin Lee / David Chmielewski / Shunzhi Wang / Ryan D Kibler / Jisu Shin / Ann Carr / Young-Jun Park / David Veesler / David Baker /
Abstract: Although the largest completely symmetric closed assembly that can be built from a single building block is the 60-subunit icosahedron, viruses can form capsid assemblies with hundreds to thousands ...Although the largest completely symmetric closed assembly that can be built from a single building block is the 60-subunit icosahedron, viruses can form capsid assemblies with hundreds to thousands of identical subunits through quasisymmetry-using the same subunit in symmetrically non-equivalent locations in the assembly. Quasisymmetric one-component assemblies could have considerable advantages for delivery of biologics because of the large internal volume achieved using only a single building block, but the design of these structures is challenging because of the inherent complexity of designing chemically identical subunits to both adopt different conformations and make different interactions in the distinct symmetrically non-equivalent locations. Here we conjectured that quasisymmetry could arise from spontaneous symmetry breaking in a system of strongly interacting building blocks with programmed curvatures and show that this principle, coupled with a design approach combining a parametric representation of cage architecture with RoseTTAFold diffusion generative modelling, can generate a rich array of quasisymmetric assemblies. Electron microscopy confirmed the structures of designed 3 ≤ T ≤ 36 cages with 180-2,160 subunits and diameters from 68 nm to 220 nm, and designed 1 < T < 3 non-icosahedral clathrin-like assemblies. Cryogenic electron microscopy structure determination showed how the global symmetry breaking associated with the formation of both hexons and pentons in the T = 3 architecture arises from symmetry breaking in the designed subunit interface. Our results indicate how the detailed architecture of complex systems can be controlled by designing overall system properties, and our approach provides a roadmap for designing large quasisymmetric assemblies for biologics delivery and other applications.
History
DepositionMay 23, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70792.png

Downloads & links

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Map

FileDownload / File: emd_70792.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM focused refinement map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.82 Å/pix.
x 720 pix.
= 1310.4 Å		1.82 Å/pix.
x 720 pix.
= 1310.4 Å		1.82 Å/pix.
x 720 pix.
= 1310.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.356
Minimum - Maximum-0.50204235 - 1.0960736
Average (Standard dev.)-0.00023024707 (±0.016955756)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 1310.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70792_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map #2

Fileemd_70792_half_map_1.map
AnnotationHalf map #2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map #1

Fileemd_70792_half_map_2.map
AnnotationHalf map #1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SLQ21

EntireName: SLQ21
Components
  • Complex: SLQ21

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Supramolecule #1: SLQ21

SupramoleculeName: SLQ21 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: E coli (bacteria)

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1074780
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

70787

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1074780
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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