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- EMDB-45735: Novel designed icosahedral nanoparticle I3-A7 -

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Entry
Database: EMDB / ID: EMD-45735
TitleNovel designed icosahedral nanoparticle I3-A7
Map dataNovel designed icosahedral nanoparticle I3-A7
Sample
  • Complex: Novel designed icosahedral nanoparticle I3-A7
    • Protein or peptide: Novel designed icosahedral nanoparticle I3-A7
KeywordsThermophile / nanoparticle / icosahedron / dehydratase / VIRUS LIKE PARTICLE
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsHaas CM / Jasti N / Dosey AM / Gillespie R / McGowan J / Allen JD / Leaf EM / Crispin M / DeForest C / Kanekiyo M / King NP
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: bioRxiv / Year: 2025
Title: From sequence to scaffold: computational design of protein nanoparticle vaccines from AlphaFold2-predicted building blocks.
Authors: Cyrus M Haas / Naveen Jasti / Annie Dosey / Joel D Allen / Rebecca Gillespie / Jackson McGowan / Elizabeth M Leaf / Max Crispin / Cole A DeForest / Masaru Kanekiyo / Neil P King /
Abstract: Self-assembling protein nanoparticles are being increasingly utilized in the design of next-generation vaccines due to their ability to induce antibody responses of superior magnitude, breadth, and ...Self-assembling protein nanoparticles are being increasingly utilized in the design of next-generation vaccines due to their ability to induce antibody responses of superior magnitude, breadth, and durability. Computational protein design offers a route to novel nanoparticle scaffolds with structural and biochemical features tailored to specific vaccine applications. Although strategies for designing new self-assembling proteins have been established, the recent development of powerful machine learning-based tools for protein structure prediction and design provides an opportunity to overcome several of their limitations. Here, we leveraged these tools to develop a generalizable method for designing novel self-assembling proteins starting from AlphaFold2 predictions of oligomeric protein building blocks. We used the method to generate six new 60-subunit protein nanoparticles with icosahedral symmetry, and single-particle cryo-electron microscopy reconstructions of three of them revealed that they were designed with atomic-level accuracy. To transform one of these nanoparticles into a functional immunogen, we reoriented its termini through circular permutation, added a genetically encoded oligomannose-type glycan, and displayed a stabilized trimeric variant of the influenza hemagglutinin receptor binding domain through a rigid linker. The resultant immunogen elicited potent receptor-blocking and neutralizing antibody responses in mice. Our results demonstrate the practical utility of machine learning-based protein modeling tools in the design of nanoparticle vaccines. More broadly, by eliminating the requirement for experimentally determined structures of protein building blocks, our method dramatically expands the number of starting points available for designing new self-assembling proteins.
History
DepositionJul 12, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45735.png

Downloads & links

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Map

FileDownload / File: emd_45735.map.gz / Format: CCP4 / Size: 791.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNovel designed icosahedral nanoparticle I3-A7
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 592 pix.
= 499.056 Å		0.84 Å/pix.
x 592 pix.
= 499.056 Å		0.84 Å/pix.
x 592 pix.
= 499.056 Å

Surface

Projections

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Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.843 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.074495815 - 0.278132
Average (Standard dev.)-0.0002085796 (±0.010273027)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions592592592
Spacing592592592
CellA=B=C: 499.056 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_45735_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_45735_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Novel designed icosahedral nanoparticle I3-A7

EntireName: Novel designed icosahedral nanoparticle I3-A7
Components
  • Complex: Novel designed icosahedral nanoparticle I3-A7
    • Protein or peptide: Novel designed icosahedral nanoparticle I3-A7

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Supramolecule #1: Novel designed icosahedral nanoparticle I3-A7

SupramoleculeName: Novel designed icosahedral nanoparticle I3-A7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Novel designed icosahedral nanoparticle I3-A7

MacromoleculeName: Novel designed icosahedral nanoparticle I3-A7 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO / EC number: phosphosulfolactate synthase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 21.152447 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGAIVVTGIP GVGKTTVMQK AAEGSPLPRV PLEGVMYGVA KRMGLVKDID EMRRLSPDVQ KEVQKKAAER IAALGDVILD THCTIKTPK GYLPGLPRWV LEKLRPSVIL LVEADPKEIY GRRLKDETRN RDPDSEEEIA EHQMMNRAAA MAYASLSGAT V KIVFNHDN RLDDAVRDAA PVLGNLEHHH HHH

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 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: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab Initio Model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 321856
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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