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- EMDB-40260: CryoEM map of a de novo designed T=4 icosahedral nanocage hierarc... -

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Basic information

Entry
Database: EMDB / ID: EMD-40260
TitleCryoEM map of a de novo designed T=4 icosahedral nanocage hierarchically built from pseudosymmetric trimers; design Ico(T=4)-4
Map datasharpened map from Local Refinement
Sample
  • Complex: Icos(T=4)-4
    • Protein or peptide: Icos(T=4)-4 chain A
    • Protein or peptide: Icos(T=4)-4 chain B
    • Protein or peptide: Icos(T=4)-4 chain C
    • Protein or peptide: Icos(T=4)-4 chain ho
Keywordsicosahedral nanocage / T=4 / T=4 icosahedra / nanomaterial / computational design / de novo / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.78 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 24, 2024-
Map releaseApr 24, 2024-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40260.png

Downloads & links

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Map

FileDownload / File: emd_40260.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map from Local Refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.33 Å/pix.
x 360 pix.
= 1199.52 Å		3.33 Å/pix.
x 360 pix.
= 1199.52 Å		3.33 Å/pix.
x 360 pix.
= 1199.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.332 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.268
Minimum - Maximum-0.1036961 - 0.71868557
Average (Standard dev.)-0.0025771467 (±0.05261018)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 1199.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map from Local Refinement

Fileemd_40260_additional_1.map
Annotationunsharpened map from Local Refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_40260_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_40260_half_map_2.map
Annotationhalf map A
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
    • Protein or peptide: Icos(T=4)-4 chain A
    • Protein or peptide: Icos(T=4)-4 chain B
    • Protein or peptide: Icos(T=4)-4 chain C
    • Protein or peptide: Icos(T=4)-4 chain ho

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

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

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Macromolecule #1: Icos(T=4)-4 chain A

MacromoleculeName: Icos(T=4)-4 chain A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSLELALKA LQILVNAAYV LAEIARDRGN EELLEKAARL AEEAARQAER IARQARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEL LEYAARLAEE AARQAIEIWA QAMEEGNQQL RTKAAHIILR AAEVLLEIAR DRGNQELLEK AASLVDAVAA LQQAAAAILE ...String:
MGSLELALKA LQILVNAAYV LAEIARDRGN EELLEKAARL AEEAARQAER IARQARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEL LEYAARLAEE AARQAIEIWA QAMEEGNQQL RTKAAHIILR AAEVLLEIAR DRGNQELLEK AASLVDAVAA LQQAAAAILE GDVEKAVRAA QEAVKAAKEA GDNDMLRAVA IAALRIAKEA EKQGNVEVAV KAARVAVEAA KQAGDNDVLR KVAEQALRIA KEAEKQGNVE VAVKAARVAV EAAKQAGDND VLRKVADQAL EIAKAALEQG DIDVAQKAMD VAVEALTQAG GSGGSHHHHH H

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Macromolecule #2: Icos(T=4)-4 chain B

MacromoleculeName: Icos(T=4)-4 chain B / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSPRLVLRA LENMVRAAHT LAEIARDNGN EEWLERAARL AEEVARRAER LAREARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEE LEYAARLAEE AARQAIEIAA QAMEEGNLEL ALKALQIIVN AAYVLAEIAR DRGNEELLEK AASLAEAAAA LAEAIAAILE ...String:
MGSPRLVLRA LENMVRAAHT LAEIARDNGN EEWLERAARL AEEVARRAER LAREARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEE LEYAARLAEE AARQAIEIAA QAMEEGNLEL ALKALQIIVN AAYVLAEIAR DRGNEELLEK AASLAEAAAA LAEAIAAILE GDVEKAVRAA QEAVKAAKEA GDNDMLRAVA IAALRIAKEA EKQGNVEVAV KAARVAVEAA KQAGDNDVLR KVAEQALRIA KEAEKQGNVE VAVKAARVAV EAAKQAGDND VLRKVAEQAL EIAKKAAEQG DVGVMQKAMD VALRAAGQAG GSGGSHHHHH H

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Macromolecule #3: Icos(T=4)-4 chain C

MacromoleculeName: Icos(T=4)-4 chain C / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSPELFLQD LRSLVEAARI LARLARQRGD EHALERAARW AEQAARQAER LARQARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEL LEYAARLAEE AARQAIEIAA QAMEEGNFEL ALEALEIINE AARVLARIAH HRGNQELLEK AASLTHASAA LSRAIAAILE ...String:
MGSPELFLQD LRSLVEAARI LARLARQRGD EHALERAARW AEQAARQAER LARQARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEL LEYAARLAEE AARQAIEIAA QAMEEGNFEL ALEALEIINE AARVLARIAH HRGNQELLEK AASLTHASAA LSRAIAAILE GDVEKAVRAA QEAVKAAKEA GDNDMLRAVA IAALRIAKEA EKQGNVEVAV KAARVAVEAA KQAGDNDVLR KVAEQALRIA KEAEKQGNVE VAVKAARVAV EAAKQAGDND VLRKVAEQAL RIAKEAEKQG NVIVAVRAAL VAAQAATEAG DQDVLRKVDE QLERILKEAR KQGGSGGSHH HHHH

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Macromolecule #4: Icos(T=4)-4 chain ho

MacromoleculeName: Icos(T=4)-4 chain ho / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSPELFLQD LRSLVEAARI LARLARQRGD EHALERAARW AEQAARQAER LARQARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEL LEYAARLAEE AARQAIEIWA QAMEEGNQQL RTKAAHIILR AAEVLLEIAR DRGNQELLEK AASLVDAVAA LQQAAAAILE ...String:
MGSPELFLQD LRSLVEAARI LARLARQRGD EHALERAARW AEQAARQAER LARQARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEL LEYAARLAEE AARQAIEIWA QAMEEGNQQL RTKAAHIILR AAEVLLEIAR DRGNQELLEK AASLVDAVAA LQQAAAAILE GDVEKAVRAA QEAVKAAKEA GDNDMLRAVA IAALRIAKEA EKQGNVEVAV KAARVAVEAA KQAGDNDVLR KVAEQALRIA KEAEKQGNVE VAVKAARVAV EAAKQAGDND VLRKVAEQAL RIAKEAEKQG NVVVATQAAI VAIQAARLAG DQDVGRKVIE QEERIAKEAR KQGGSGGSHH 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 / 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: 12.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 6896
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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