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- EMDB-28027: Structure of a nanoparticle with icosahedral symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-28027
TitleStructure of a nanoparticle with icosahedral symmetry
Map dataPost-processed map
Sample
  • Complex: I3-01
    • Protein or peptide: Designed I3-01 icosahedron
Function / homology4-hydroxy-2-oxoglutarate aldolase / 4-hydroxy-2-oxoglutarate aldolase activity / 2-dehydro-3-deoxy-phosphogluconate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / KDPG/KHG aldolase / KDPG and KHG aldolase / Aldolase-type TIM barrel / 4-Hydroxy-2-oxoglutarate aldolase / 2-dehydro-3-deoxyphosphogluconate aldolase
Function and homology information
Biological speciesThermotoga maritima MSB8 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMcCarthy S / Gonen S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Heliyon / Year: 2022
Title: Improved interface packing and design opportunities revealed by CryoEM analysis of a designed protein nanocage.
Authors: Stephen McCarthy / Shane Gonen /
Abstract: Symmetric protein assemblies play important roles in nature which makes them an attractive target for engineering. symmetric protein complexes can be created through computational protein design to ...Symmetric protein assemblies play important roles in nature which makes them an attractive target for engineering. symmetric protein complexes can be created through computational protein design to tailor their properties from first principles, and recently several protein nanocages have been created by bringing together protein components through hydrophobic interactions. Accurate experimental structures of newly-developed proteins are essential to validate their design, improve assembly stability, and tailor downstream applications. We describe the CryoEM structure of the nanocage I3-01, at an overall resolution of 3.5 Å. I3-01, comprising 60 aldolase subunits arranged with icosahedral symmetry, has resisted high-resolution characterization. Some key differences between the refined structure and the original design are identified, such as improved packing of hydrophobic sidechains, providing insight to the resistance of I3-01 to high-resolution averaging. Based on our analysis, we suggest factors important in the design and structural processing of new assemblies.
History
DepositionSep 2, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateJan 11, 2023-
Current statusJan 11, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28027.png

Downloads & links

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Map

FileDownload / File: emd_28027.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed map
Voxel sizeX=Y=Z: 1.31 Å
Density
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.07699508 - 0.13069205
Average (Standard dev.)0.00021671712 (±0.0034348457)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 471.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map 1

Fileemd_28027_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_28027_half_map_2.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : I3-01

EntireName: I3-01
Components
  • Complex: I3-01
    • Protein or peptide: Designed I3-01 icosahedron

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Supramolecule #1: I3-01

SupramoleculeName: I3-01 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermotoga maritima MSB8 (bacteria)

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Macromolecule #1: Designed I3-01 icosahedron

MacromoleculeName: Designed I3-01 icosahedron / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO / EC number: 2-dehydro-3-deoxy-phosphogluconate aldolase
Source (natural)Organism: Thermotoga maritima MSB8 (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Molecular weightTheoretical: 21.660584 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEELFKKHKI VAVLRANSVE EAKKKALAVF LGGVHLIEIT FTVPDADTVI KELSFLKEMG AIIGAGTVTS VEQCRKAVES GAEFIVSPH LDEEISQFCK EKGVFYMPGV MTPTELVKAM KLGHTILKLF PGEVVGPQFV KAMKGPFPNV KFVPTGGVNL D NVCEWFKA ...String:
MEELFKKHKI VAVLRANSVE EAKKKALAVF LGGVHLIEIT FTVPDADTVI KELSFLKEMG AIIGAGTVTS VEQCRKAVES GAEFIVSPH LDEEISQFCK EKGVFYMPGV MTPTELVKAM KLGHTILKLF PGEVVGPQFV KAMKGPFPNV KFVPTGGVNL D NVCEWFKA GVLAVGVGSA LVKGTPVEVA EKAKAFVEKI RGC

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Stochastic gradient descent from 2D averages
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 147349

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8ed3:
Structure of a nanoparticle with icosahedral symmetry

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