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- EMDB-47039: Pseudosymmetric protein nanocage GI16-F7 -

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Basic information

Entry
Database: EMDB / ID: EMD-47039
TitlePseudosymmetric protein nanocage GI16-F7
Map data
Sample
  • Complex: Pseudosymmetric protein nanocages: GI9-F7 nanocage
    • Protein or peptide: Pseudosymmetric protein nanocage GI16-F7 A Chain
    • Protein or peptide: Pseudosymmetric protein nanocage GI16-F7 B Chain
    • Protein or peptide: Pseudosymmetric protein nanocage GI16-F7 C Chain
KeywordsFusion protein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / pseudosymmetric protein nanocages / VIRAL PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.9 Å
AuthorsPark YJ / Dowling QM / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / King NP / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI158186 United States
CitationJournal: Nature / Year: 2025
Title: Hierarchical design of pseudosymmetric protein nanocages.
Authors: Quinton M Dowling / Young-Jun Park / Chelsea N Fries / Neil C Gerstenmaier / Sebastian Ols / Erin C Yang / Adam J Wargacki / Annie Dosey / Yang Hsia / Rashmi Ravichandran / Carl D Walkey / ...Authors: Quinton M Dowling / Young-Jun Park / Chelsea N Fries / Neil C Gerstenmaier / Sebastian Ols / Erin C Yang / Adam J Wargacki / Annie Dosey / Yang Hsia / Rashmi Ravichandran / Carl D Walkey / Anika L Burrell / David Veesler / David Baker / Neil P King /
Abstract: Discrete protein assemblies ranging from hundreds of kilodaltons to hundreds of megadaltons in size are a ubiquitous feature of biological systems and perform highly specialized functions. Despite ...Discrete protein assemblies ranging from hundreds of kilodaltons to hundreds of megadaltons in size are a ubiquitous feature of biological systems and perform highly specialized functions. Despite remarkable recent progress in accurately designing new self-assembling proteins, the size and complexity of these assemblies has been limited by a reliance on strict symmetry. Here, inspired by the pseudosymmetry observed in bacterial microcompartments and viral capsids, we developed a hierarchical computational method for designing large pseudosymmetric self-assembling protein nanomaterials. We computationally designed pseudosymmetric heterooligomeric components and used them to create discrete, cage-like protein assemblies with icosahedral symmetry containing 240, 540 and 960 subunits. At 49, 71 and 96 nm diameter, these nanocages are the largest bounded computationally designed protein assemblies generated to date. More broadly, by moving beyond strict symmetry, our work substantially broadens the variety of self-assembling protein architectures that are accessible through design.
History
DepositionSep 17, 2024-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47039.png

Downloads & links

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Map

FileDownload / File: emd_47039.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.84 Å/pix.
x 600 pix.
= 1704. Å		2.84 Å/pix.
x 600 pix.
= 1704. Å		2.84 Å/pix.
x 600 pix.
= 1704. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.3
Minimum - Maximum-0.21439731 - 1.7495959
Average (Standard dev.)0.006968156 (±0.122478835)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 1704.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_47039_additional_1.map
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Half map: #1

Fileemd_47039_half_map_1.map
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Half map: #2

Fileemd_47039_half_map_2.map
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Sample components

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Entire : Pseudosymmetric protein nanocages: GI9-F7 nanocage

EntireName: Pseudosymmetric protein nanocages: GI9-F7 nanocage
Components
  • Complex: Pseudosymmetric protein nanocages: GI9-F7 nanocage
    • Protein or peptide: Pseudosymmetric protein nanocage GI16-F7 A Chain
    • Protein or peptide: Pseudosymmetric protein nanocage GI16-F7 B Chain
    • Protein or peptide: Pseudosymmetric protein nanocage GI16-F7 C Chain

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Supramolecule #1: Pseudosymmetric protein nanocages: GI9-F7 nanocage

SupramoleculeName: Pseudosymmetric protein nanocages: GI9-F7 nanocage / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Pseudosymmetric protein nanocage GI16-F7 A Chain

MacromoleculeName: Pseudosymmetric protein nanocage GI16-F7 A Chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSHHHHHHGS EKAAKAEEAA RKMEELFKEH KIVAVLRANS VEEAKKKALA VFLGGVHLIE ITFTVPDADT VIKELSFLKE MGAIIGAGTV TSVEQCREAV ESGAEFIVSP HLDEEISQFC KEEGVFYMPG VMTPTELYKA MKLGHTILKL FPGEVVGPQF VEAMKGPFPN ...String:
GSHHHHHHGS EKAAKAEEAA RKMEELFKEH KIVAVLRANS VEEAKKKALA VFLGGVHLIE ITFTVPDADT VIKELSFLKE MGAIIGAGTV TSVEQCREAV ESGAEFIVSP HLDEEISQFC KEEGVFYMPG VMTPTELYKA MKLGHTILKL FPGEVVGPQF VEAMKGPFPN VKFVPTGGVN LDNVCEWFEA GVLAVGVGSA LVEGTPVEVA EKAKAFVEKI EGCTE

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Macromolecule #2: Pseudosymmetric protein nanocage GI16-F7 B Chain

MacromoleculeName: Pseudosymmetric protein nanocage GI16-F7 B Chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKMEELFKEH KIVAVLRANS VEEAISKALA VFAGGVHLIE ITFTVPDADQ VIKELEFLKE AGAIIGAGTV TSVEQCREAV ESGAEFIVSF HLDEEISQFC KEEGVFYMPG VMTPTELVKA MKLGHTILKL VPGEVVGPQF VEAMKGPFPN VKFVPTGGVN LDNVCEWFEA ...String:
MKMEELFKEH KIVAVLRANS VEEAISKALA VFAGGVHLIE ITFTVPDADQ VIKELEFLKE AGAIIGAGTV TSVEQCREAV ESGAEFIVSF HLDEEISQFC KEEGVFYMPG VMTPTELVKA MKLGHTILKL VPGEVVGPQF VEAMKGPFPN VKFVPTGGVN LDNVCEWFEA GVLAVGVGSA LVEGEPAEVA ELAIRFVEKI RGCTE

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Macromolecule #3: Pseudosymmetric protein nanocage GI16-F7 C Chain

MacromoleculeName: Pseudosymmetric protein nanocage GI16-F7 C Chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
SequenceString: MKMEELFKEH KIVAVLRANS REEAIEIALA VFAGGVHLIE ITFTVPDADE VIKRLEMLKR AGAIIGAGTV TSVEQCREAV ESGAEFIVSP HLDEEISQFC KEEGVFYMPG VMTPTELVKA MKLGHTILKL FPGEVVGPQF VEAMKGPFPN VKFVPTGGVN LDNVCEWFEA ...String:
MKMEELFKEH KIVAVLRANS REEAIEIALA VFAGGVHLIE ITFTVPDADE VIKRLEMLKR AGAIIGAGTV TSVEQCREAV ESGAEFIVSP HLDEEISQFC KEEGVFYMPG VMTPTELVKA MKLGHTILKL FPGEVVGPQF VEAMKGPFPN VKFVPTGGVN LDNVCEWFEA GVLAVGVGSA LVEGKPSEVA EKARRFVKKI RGCTEGSLEH HHHHH

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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: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 14.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1083
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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