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- EMDB-45736: Novel designed icosahedral nanoparticle I3-D12 -

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Basic information

Entry
Database: EMDB / ID: EMD-45736
TitleNovel designed icosahedral nanoparticle I3-D12
Map dataNovel designed icosahedral nanoparticle I3-D12
Sample
  • Complex: Novel designed icosahedral nanoparticle I3-D12
    • Protein or peptide: Phosphosulfolactate synthase
KeywordsThermophile / nanoparticle / icosahedron / dehydratase / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


phosphosulfolactate synthase / coenzyme M biosynthetic process / phosphosulfolactate synthase activity / sulfopyruvate decarboxylase activity
Similarity search - Function
Phosphosulpholactate synthase / (2R)-phospho-3-sulpholactate synthase, ComA / (2R)-phospho-3-sulpholactate synthase, ComA superfamily / (2R)-phospho-3-sulfolactate synthase (ComA) / Aldolase-type TIM barrel
Similarity search - Domain/homology
Phosphosulfolactate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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: To Be Published
Title: Computational design of protein nanoparticle vaccine scaffolds from sequence alone
Authors: Haas CM / Jasti N / Dosey AM / Gillespie R / Allen JD / 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_45736.png

Downloads & links

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Map

FileDownload / File: emd_45736.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNovel designed icosahedral nanoparticle I3-D12
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 600 pix.
= 505.8 Å		0.84 Å/pix.
x 600 pix.
= 505.8 Å		0.84 Å/pix.
x 600 pix.
= 505.8 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: 0.14
Minimum - Maximum-0.09714371 - 0.4086359
Average (Standard dev.)-0.00016562059 (±0.016772846)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 505.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A icosahedral nanoparticle I3-D12

Fileemd_45736_half_map_1.map
AnnotationHalf Map A icosahedral nanoparticle I3-D12
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B icosahedral nanoparticle I3-D12

Fileemd_45736_half_map_2.map
AnnotationHalf Map B icosahedral nanoparticle I3-D12
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-D12

EntireName: Novel designed icosahedral nanoparticle I3-D12
Components
  • Complex: Novel designed icosahedral nanoparticle I3-D12
    • Protein or peptide: Phosphosulfolactate synthase

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Supramolecule #1: Novel designed icosahedral nanoparticle I3-D12

SupramoleculeName: Novel designed icosahedral nanoparticle I3-D12 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Phosphosulfolactate synthase

MacromoleculeName: Phosphosulfolactate synthase / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 29.228348 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKAFEFLYED FQRGLTVVLD KGLPPKFVED YLKVCGDYID FVKFGWGTSA VIDRDVVKEK INYYKDWGIK VYPGGTLFEY AYSKGEAAE FIAECKKLGF EAVEISDGSS DISLDDRKAA IWGAKWAGFM VLTEVGKKMP DKDKQLTIDD RIKLINFDLD A GADYVIIE ...String:
MKAFEFLYED FQRGLTVVLD KGLPPKFVED YLKVCGDYID FVKFGWGTSA VIDRDVVKEK INYYKDWGIK VYPGGTLFEY AYSKGEAAE FIAECKKLGF EAVEISDGSS DISLDDRKAA IWGAKWAGFM VLTEVGKKMP DKDKQLTIDD RIKLINFDLD A GADYVIIE GRESGKGIGL FDKEGKVKEN ELDVLAKNVD INKVIFEAPQ KSQQVAFILK FGSSVNLANI AFDEVISLET LR RGLRGDT FGKVLEHHHH HH

UniProtKB: Phosphosulfolactate synthase

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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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 165931
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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