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- EMDB-40268: CryoEM map of a de novo designed T=4 octahedral nanocage hierarch... -

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Basic information

Entry
Database: EMDB / ID: EMD-40268
TitleCryoEM map of a de novo designed T=4 octahedral nanocage hierarchically built from pseudosymmetric trimers; design Oct(T=4)-3
Map datasharpened map using DeepEMhancer
Sample
  • Complex: Oct(T=4)-3
    • Protein or peptide: Oct(T=4)-3 chain A
    • Protein or peptide: Oct(T=4)-3 chain B
    • Protein or peptide: Oct(T=4)-3 chain C
    • Protein or peptide: Oct(T=4)-3 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: 6.87 Å
AuthorsPhilomin A / Borst AJ / Kibler RD
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_40268.png

Downloads & links

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Map

FileDownload / File: emd_40268.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map using DeepEMhancer
Voxel sizeX=Y=Z: 2.36 Å
Density
Contour LevelBy AUTHOR: 0.103
Minimum - Maximum-0.0017326495 - 1.6085112
Average (Standard dev.)0.0021726172 (±0.028964581)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 707.99994 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_40268_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_40268_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_40268_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 : Oct(T=4)-3

EntireName: Oct(T=4)-3
Components
  • Complex: Oct(T=4)-3
    • Protein or peptide: Oct(T=4)-3 chain A
    • Protein or peptide: Oct(T=4)-3 chain B
    • Protein or peptide: Oct(T=4)-3 chain C
    • Protein or peptide: Oct(T=4)-3 chain ho

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Supramolecule #1: Oct(T=4)-3

SupramoleculeName: Oct(T=4)-3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: A hierarchically designed T=4 octahedral nanocage
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Oct(T=4)-3 chain A

MacromoleculeName: Oct(T=4)-3 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 KQAGDQDVLL KVATQAARIA LEAIKQGNLE VKLEALKVAQ EALKQTGGSG GSHHHHHH

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Macromolecule #2: Oct(T=4)-3 chain B

MacromoleculeName: Oct(T=4)-3 chain B / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
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 KQAGDQDVLK KVAAQAARIM LEAIKQGNTE VALEALKVAQ EALKQTGGSG GSHHHHHH

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

MacromoleculeName: Oct(T=4)-3 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 KEAEKQGNVI VAMKAIDVAV EAAGQAGDID VIKKVADQTQ RIVDEWLKQG

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Macromolecule #4: Oct(T=4)-3 chain ho

MacromoleculeName: Oct(T=4)-3 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 KEAEKQGNVY VAAKAVQVAA EAAKQAGDID VLKKVIGQTQ RIRDEWVKQG GSGGSHHHHH H

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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

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.7000000000000001 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2

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Image processing

Startup modelType of model: OTHER / Details: Ab initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29069
FSC plot (resolution estimation)

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