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- EMDB-70685: Two Component Protein Nano-Particle (T=3). De Novo Design, Comput... -

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Basic information

Entry
Database: EMDB / ID: EMD-70685
TitleTwo Component Protein Nano-Particle (T=3). De Novo Design, Computationally Relaxed into Low Resolution Subtomogram Averaged CryoEM Map with Icosahedral Symmetry Applied
Map data
Sample
  • Complex: Protein structure is equivalent to a C60 fullerene and has the general shape of a soccer ball with 12 pentagonal and 20 hexagonal facets. There are a total of 60 vertices (C3-A) and 90 edges (C2-B)
    • Protein or peptide: C2-B
    • Protein or peptide: C3-A
KeywordsGoldberg icosahedron / C60 / Fullerene / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsubtomogram averaging / cryo EM / Resolution: 31.6 Å
AuthorsDiMaio F / Chmielewski D / Weidle C
Funding support United States, France, 8 items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)HDTRA1-19-1-0003 United States
Burroughs Wellcome Fund United States
Human Frontier Science Program (HFSP)RGP0061/2019 France
Bill & Melinda Gates FoundationINV-043758 United States
Bill & Melinda Gates FoundationOPP1156262 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG063845 United States
Department of Energy (DOE, United States)KP1607011 United States
CitationJournal: Nature / Year: 2026
Title: De novo design of quasisymmetric two-component protein cages.
Authors: Shunzhi Wang / Ying Xie / David Chemielewski / Connor Weidle / Tong Shu / Green Ahn / Ryan D Kibler / Cindy Hernandez / Wei Chen / David Camilo Duran / Ann Carr / Asim K Bera / Sangmin Lee / ...Authors: Shunzhi Wang / Ying Xie / David Chemielewski / Connor Weidle / Tong Shu / Green Ahn / Ryan D Kibler / Cindy Hernandez / Wei Chen / David Camilo Duran / Ann Carr / Asim K Bera / Sangmin Lee / Justin Decarreau / Alex Kang / Evans Brackenbrough / Emily Joyce / Kejia Wu / Andrew J Borst / Andrew Favor / Buwei Huang / Frank DiMaio / Liam J Holt / David Baker /
Abstract: Quasisymmetric icosahedral viral capsids achieve larger sizes than possible with strictly symmetric icosahedra by tessellating pentagons and hexagons using a single subunit that adopts different ...Quasisymmetric icosahedral viral capsids achieve larger sizes than possible with strictly symmetric icosahedra by tessellating pentagons and hexagons using a single subunit that adopts different conformations in symmetrically non-equivalent locations. Recapitulating such quasisymmetric architectures through computational design is a considerable challenge in nanomaterials engineering. Here we introduce a computational design strategy based on geometric frustration to generate two-component, quasisymmetric protein cages with customizable properties. We designed complementary trimeric and dimeric protein components that co-assemble into positively curved local hexagonal assemblies. Hexagonal lattices cannot tile spherical surfaces; instead, the components form closed sphere-like cage assemblies through incorporation of curvature-inducing pentagonal defects, as evidenced by electron microscopy. By designing dimers that encode different local curvatures, we programmed cage dimensions ranging from 40 to over 200 nm in diameter and with molecular weights from 2 MDa to over 50 MDa, comparable with natural virus capsids. We further functionalized these large cages with additional protein domains to enable ribonucleoprotein cargo loading and cellular uptake. Fluorescently labelled cage assemblies expressed in mammalian cells function as rheological probes and cargo recruiters, enabling a systematic study of size-dependent cytoplasmic diffusion and protein localization. Thus, the quasi-symmetry that has long fascinated structural biologists can now be achieved by computational protein design, with immediate applications to biologics delivery and molecular cell biology.
History
DepositionMay 17, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70685.png

Downloads & links

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Map

FileDownload / File: emd_70685.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.62 Å/pix.
x 240 pix.
= 868.8 Å		3.62 Å/pix.
x 240 pix.
= 868.8 Å		3.62 Å/pix.
x 240 pix.
= 868.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.62 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1854.0
Minimum - Maximum1.0 - 4095.0
Average (Standard dev.)1211.762199999999893 (±264.15179999999998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 868.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_70685_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70685_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Protein structure is equivalent to a C60 fullerene and has the ge...

EntireName: Protein structure is equivalent to a C60 fullerene and has the general shape of a soccer ball with 12 pentagonal and 20 hexagonal facets. There are a total of 60 vertices (C3-A) and 90 edges (C2-B)
Components
  • Complex: Protein structure is equivalent to a C60 fullerene and has the general shape of a soccer ball with 12 pentagonal and 20 hexagonal facets. There are a total of 60 vertices (C3-A) and 90 edges (C2-B)
    • Protein or peptide: C2-B
    • Protein or peptide: C3-A

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Supramolecule #1: Protein structure is equivalent to a C60 fullerene and has the ge...

SupramoleculeName: Protein structure is equivalent to a C60 fullerene and has the general shape of a soccer ball with 12 pentagonal and 20 hexagonal facets. There are a total of 60 vertices (C3-A) and 90 edges (C2-B)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: C2-B

MacromoleculeName: C2-B / type: protein_or_peptide / ID: 1 / Number of copies: 180 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.591434 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
PTLRVEIEGP AADVAALLRG VAELAAERAP KLAPVVAVIA DFVASRPGPV RVRVEMGDGV LRVVLEGLHI KQQRQLYRDV RETSKKQGV ETEIEVEGDT VTIVVRELEH HHHHH

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Macromolecule #2: C3-A

MacromoleculeName: C3-A / type: protein_or_peptide / ID: 2 / Number of copies: 180 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 33.381504 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: SDEAIKRLLE ELRASTAELK RATASLRAIT EELKKNPSED ALVEHNRAIV EHNAIIVENN RIIAAVLEAI VAEFILAKAR LLVWEARKK GNPEEVLEAA KKALRVAEEA AKAGIEAIFK AAAEAALEIA MRLIDLATKK GDPDLVREAQ KVAERVAELA D KNGDEEVK ...String:
SDEAIKRLLE ELRASTAELK RATASLRAIT EELKKNPSED ALVEHNRAIV EHNAIIVENN RIIAAVLEAI VAEFILAKAR LLVWEARKK GNPEEVLEAA KKALRVAEEA AKAGIEAIFK AAAEAALEIA MRLIDLATKK GDPDLVREAQ KVAERVAELA D KNGDEEVK LKAYAAAVAA EIIRRIETLK RSGSSYEDIR QTLRETLERI IEELKRRGVD SSQIVWAIIY VAVAVMGVTM ET HKSGNEV KVVIKGLHES QQEELLELVL RAAELAGVRV RIRFKGDTVT IVVRGLEHHH HHH

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMTris-HCltris(hydroxymethyl)aminomethane Hydrochloric Acid
300.0 mMNaClSodium Chloride

Details: 25 mM Tris-HCl and 300 mM NaCl (pH 8)
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 39.0 kPa / Details: 15mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.68 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 22000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 31.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 / Number subtomograms used: 462
ExtractionNumber tomograms: 462 / Number images used: 599
CTF correctionSoftware - Name: EMAN2 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: EMAN2 / Details: 3D tomogram volumes using e2_tomogram.py

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: Computational Design
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9op9:
Two Component Protein Nano-Particle (T=3). De Novo Design, Computationally Relaxed into Low Resolution Subtomogram Averaged CryoEM Map with Icosahedral Symmetry Applied

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