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- EMDB-28028: I3-01 in an expanded conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-28028
TitleI3-01 in an expanded conformation
Map dataExpanded map
Sample
  • Complex: I3-01
    • Protein or peptide: Designed I3-01 icosahedron
KeywordsProtein design / nanoparticle / DE NOVO PROTEIN
Biological speciesThermotoga maritima MSB8 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJul 12, 2023-
Current statusJul 12, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28028.png

Downloads & links

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Map

FileDownload / File: emd_28028.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationExpanded map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 360 pix.
= 471.6 Å		1.31 Å/pix.
x 360 pix.
= 471.6 Å		1.31 Å/pix.
x 360 pix.
= 471.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.028143732 - 0.061149497
Average (Standard dev.)0.00021111277 (±0.0023156065)
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-map1

Fileemd_28028_half_map_1.map
AnnotationHalf-map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map2

Fileemd_28028_half_map_2.map
AnnotationHalf-map2
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 / 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 / Enantiomer: LEVO
Source (natural)Organism: Thermotoga maritima MSB8 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEELFKKHKI VAVLRANSVE EAKKKALAVF LGGVHLIEIT FTVPDADTVI KELSFLKEMG AIIGAGTVTS VEQCRKAVES GAEFIVSPHL DEEISQFCKE KGVFYMPGVM TPTELVKAMK LGHTILKLFP GEVVGPQFVK AMKGPFPNVK FVPTGGVNLD NVCEWFKAGV ...String:
MEELFKKHKI VAVLRANSVE EAKKKALAVF LGGVHLIEIT FTVPDADTVI KELSFLKEMG AIIGAGTVTS VEQCRKAVES GAEFIVSPHL DEEISQFCKE KGVFYMPGVM TPTELVKAMK LGHTILKLFP GEVVGPQFVK AMKGPFPNVK FVPTGGVNLD NVCEWFKAGV LAVGVGSALV KGTPVEVAEK AKAFVEKIRG C

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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 K2 SUMMIT (4k x 4k) / Average electron dose: 2.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
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
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33472
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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