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- EMDB-45734: Novel designed icosahedral nanoparticle I3-A6 -

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Basic information

Entry
Database: EMDB / ID: EMD-45734
TitleNovel designed icosahedral nanoparticle I3-A6
Map dataNovel designed icosahedral nanoparticle I3-A6
Sample
  • Complex: Novel designed icosahedral nanoparticle I3-A6
    • Protein or peptide: I3-A6
KeywordsThermophile / nanoparticle / icosahedron / dehydratase / VIRUS LIKE PARTICLE
Biological speciesEscherichia coli (E. coli) / Escherichia coli BL21 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsHaas CM / Jasti N / Dosey AM / Gillespie R / 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: To Be Published
Title: From sequence to scaffold: computational design of protein nanoparticle vaccines from AlphaFold2-predicted building blocks
Authors: Haas CM / Jasti N / Dosey AM / Allen JD / Gillespie R / McGowan J / Leaf EM / Crispin M / DeForest C / Kanekiyo M / King NP
History
DepositionJul 12, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45734.png

Downloads & links

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Map

FileDownload / File: emd_45734.map.gz / Format: CCP4 / Size: 791.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNovel designed icosahedral nanoparticle I3-A6
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.843 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.08066982 - 0.45142707
Average (Standard dev.)-0.0009576043 (±0.01712046)
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: Novel designed icosahedral nanoparticle I3-A6

Fileemd_45734_half_map_1.map
AnnotationNovel designed icosahedral nanoparticle I3-A6
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Novel designed icosahedral nanoparticle I3-A6

Fileemd_45734_half_map_2.map
AnnotationNovel designed icosahedral nanoparticle I3-A6
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Novel designed icosahedral nanoparticle I3-A6

EntireName: Novel designed icosahedral nanoparticle I3-A6
Components
  • Complex: Novel designed icosahedral nanoparticle I3-A6
    • Protein or peptide: I3-A6

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Supramolecule #1: Novel designed icosahedral nanoparticle I3-A6

SupramoleculeName: Novel designed icosahedral nanoparticle I3-A6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: I3-A6

MacromoleculeName: I3-A6 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BL21 (bacteria)
Molecular weightTheoretical: 20.963756 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MTDEPVATEE PAARDEVRRA EALGGQAAEQ LAMKILVING PNINFLGIRE KGIYGPLNYD DLVEMIKGTA KGLKVKVEVF QSNHEGAII DKLQEAYYND VDGIVINPGA FTHYSYAVRD ALASIAAIPK IEVHISNVHT REEFRHTSVT VPVCQGEVVG L GLGGYLAA ...String:
MTDEPVATEE PAARDEVRRA EALGGQAAEQ LAMKILVING PNINFLGIRE KGIYGPLNYD DLVEMIKGTA KGLKVKVEVF QSNHEGAII DKLQEAYYND VDGIVINPGA FTHYSYAVRD ALASIAAIPK IEVHISNVHT REEFRHTSVT VPVCQGEVVG L GLGGYLAA MGMLVEMTKS NGSWGSLEHH HHHH

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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

MicroscopeFEI TITAN 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: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 290122
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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