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- EMDB-47038: Pseudosymmetric protein nanocage GI9-F7 (local refinement) -

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Basic information

Entry
Database: EMDB / ID: EMD-47038
TitlePseudosymmetric protein nanocage GI9-F7 (local refinement)
Map data
Sample
  • Complex: Pseudosymmetric protein nanocages: GI9-F7 nanocage
    • Protein or peptide: Pseudosymmetric protein nanocage GI9-F7 A chain
    • Protein or peptide: Pseudosymmetric protein nanocage GI9-F7 C chain
    • Protein or peptide: Pseudosymmetric protein nanocage GI9-F7 B 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: 4.0 Å
AuthorsPark YJ / Dowling QM / King NP / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / 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) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47038.png

Downloads & links

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Map

FileDownload / File: emd_47038.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.69 Å/pix.
x 720 pix.
= 1213.92 Å		1.69 Å/pix.
x 720 pix.
= 1213.92 Å		1.69 Å/pix.
x 720 pix.
= 1213.92 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.686 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.8
Minimum - Maximum-4.4105883 - 8.02094
Average (Standard dev.)0.0022871546 (±0.07800081)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 1213.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_47038_additional_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_47038_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47038_half_map_2.map
Projections & Slices
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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 GI9-F7 A chain
    • Protein or peptide: Pseudosymmetric protein nanocage GI9-F7 C chain
    • Protein or peptide: Pseudosymmetric protein nanocage GI9-F7 B 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 GI9-F7 A chain

MacromoleculeName: Pseudosymmetric protein nanocage GI9-F7 A chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 24.330975 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSHHHHHHGS EKAAKAEEAA RKMEELFKEH KIVAVLRANS VEEAKKKALA VFLGGVHLIE ITFTVPDADT VIKELSFLKE MGAIIGAGT VTSVEQCREA VESGAEFIVS PHLDEEISQF CKEEGVFYMP GVMTPTELYK AMKLGHTILK LFPGEVVGPQ F VEAMKGPF ...String:
GSHHHHHHGS EKAAKAEEAA RKMEELFKEH KIVAVLRANS VEEAKKKALA VFLGGVHLIE ITFTVPDADT VIKELSFLKE MGAIIGAGT VTSVEQCREA VESGAEFIVS PHLDEEISQF CKEEGVFYMP GVMTPTELYK AMKLGHTILK LFPGEVVGPQ F VEAMKGPF PNVKFVPTGG VNLDNVCEWF EAGVLAVGVG SALVEGTPVE VAEKAKAFVE KIEGCTE

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Macromolecule #2: Pseudosymmetric protein nanocage GI9-F7 C chain

MacromoleculeName: Pseudosymmetric protein nanocage GI9-F7 C chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.530266 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKMEELFKEH KIVAVLRANS REEAIEIALA VFAGGVHLIE ITFTVPDADE VIKRLEMLKR AGAIIGAGTV TSVEQCREAV ESGAEFIVS PHLDEEISQF CKEEGVFYMP GVMTPTELVK AMKLGHTILK LFPGEVVGPQ FVEAMKGPFP NVKFVPTGGV N LDNVCEWF ...String:
MKMEELFKEH KIVAVLRANS REEAIEIALA VFAGGVHLIE ITFTVPDADE VIKRLEMLKR AGAIIGAGTV TSVEQCREAV ESGAEFIVS PHLDEEISQF CKEEGVFYMP GVMTPTELVK AMKLGHTILK LFPGEVVGPQ FVEAMKGPFP NVKFVPTGGV N LDNVCEWF EAGVLAVGVG SALVEGKPSE VAEKARRFVK KIRGCTEGSL EHHHHHH

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Macromolecule #3: Pseudosymmetric protein nanocage GI9-F7 B chain

MacromoleculeName: Pseudosymmetric protein nanocage GI9-F7 B chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 22.115564 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKMEELFKEH KIVAVLRANS VEEAISKALA VFAGGVHLIE ITFTVPDADQ VIKELEFLKE AGAIIGAGTV TSVEQCREAV ESGAEFIVS FHLDEEISQF CKEEGVFYMP GVMTPTELVK AMKLGHTILK LVPGEVVGPQ FVEAMKGPFP NVKFVPTGGV N LDNVCEWF ...String:
MKMEELFKEH KIVAVLRANS VEEAISKALA VFAGGVHLIE ITFTVPDADQ VIKELEFLKE AGAIIGAGTV TSVEQCREAV ESGAEFIVS FHLDEEISQF CKEEGVFYMP GVMTPTELVK AMKLGHTILK LVPGEVVGPQ FVEAMKGPFP NVKFVPTGGV N LDNVCEWF EAGVLAVGVG SALVEGEPAE VAELAIRFVE KIRGCTE

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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: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 795360
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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