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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: Wang S / Xie Y / Chemielewski D / Weidle C / Hernandez C / Chen W / Ahn G / Duran DC / Bera AK / Bethel N / Decarreau J / Tong S / Kang A / Brackenbrough E / Joyce E / Lee S / Wu K / Borst ...Authors: Wang S / Xie Y / Chemielewski D / Weidle C / Hernandez C / Chen W / Ahn G / Duran DC / Bera AK / Bethel N / Decarreau J / Tong S / Kang A / Brackenbrough E / Joyce E / Lee S / Wu K / Borst AJ / Favor A / Buwei H / DiMaio F / Holt L / Baker D
History
DepositionMay 17, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 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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