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- EMDB-40267: CryoEM map of a T=1 off-target state of design Ico(T=4)-4 -

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Basic information

Entry
Database: EMDB / ID: EMD-40267
TitleCryoEM map of a T=1 off-target state of design Ico(T=4)-4
Map datasharpened map from deepEMhancer
Sample
  • Complex: Icos(T=4)-4
Keywordsicosahedral nanocage / T=4 / T=4 icosahedra / T=1 / T=1 icosahedra / off-target / nanomaterial / computational design / de novo / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.54 Å
AuthorsBorst AJ / Kibler RD / Lee S
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Design of four component T=4 tetrahedral, octahedral, and icosahedral protein nanocages through programmed symmetry breaking
Authors: Lee S / Kibler RD / Hsia Y / Borst AJ / Philomin A / Kennedy MA / Stoddard B / Baker D
History
DepositionMar 31, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40267.png

Downloads & links

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Map

FileDownload / File: emd_40267.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map from deepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.56 Å/pix.
x 360 pix.
= 920.52 Å		2.56 Å/pix.
x 360 pix.
= 920.52 Å		2.56 Å/pix.
x 360 pix.
= 920.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.557 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.226
Minimum - Maximum-0.0001407214 - 1.3843389
Average (Standard dev.)0.0010108374 (±0.021511747)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 920.51996 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map from final Non-Uniform Refinement

Fileemd_40267_additional_1.map
Annotationunsharpened map from final Non-Uniform Refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A from final Non-Uniform Refinement

Fileemd_40267_half_map_1.map
Annotationhalf map A from final Non-Uniform Refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B from final Non-Uniform Refinement

Fileemd_40267_half_map_2.map
Annotationhalf map B from final Non-Uniform Refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Icos(T=4)-4

EntireName: Icos(T=4)-4
Components
  • Complex: Icos(T=4)-4

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Supramolecule #1: Icos(T=4)-4

SupramoleculeName: Icos(T=4)-4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / Details: A hierarchically designed T=4 icosahedral nanocage
Source (natural)Organism: synthetic construct (others)

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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 / Details: 25mM Tris, 300mM NaCl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 6678 / Average electron dose: 61.463 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1172
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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