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- EMDB-15720: cryo-EM structure of carboxysome mini-shell: icosahedral structur... -

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Basic information

Entry
Database: EMDB / ID: EMD-15720
Titlecryo-EM structure of carboxysome mini-shell: icosahedral structure from C1 construct (T=7)
Map datamain map
Sample
  • Complex: mini-shell assembly from Halothiobacillus neapolitanus in icosahedral form
KeywordsCarboxysome / mini-shell / icosahedral / virus-like particle / STRUCTURAL PROTEIN
Biological speciesHalothiobacillus neapolitanus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsNi T / Ng PC / Liu L / Zhang P
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Intrinsically disordered CsoS2 acts as a general molecular thread for α-carboxysome shell assembly.
Authors: Tao Ni / Qiuyao Jiang / Pei Cing Ng / Juan Shen / Hao Dou / Yanan Zhu / Julika Radecke / Gregory F Dykes / Fang Huang / Lu-Ning Liu / Peijun Zhang /
Abstract: Carboxysomes are a paradigm of self-assembling proteinaceous organelles found in nature, offering compartmentalisation of enzymes and pathways to enhance carbon fixation. In α-carboxysomes, the ...Carboxysomes are a paradigm of self-assembling proteinaceous organelles found in nature, offering compartmentalisation of enzymes and pathways to enhance carbon fixation. In α-carboxysomes, the disordered linker protein CsoS2 plays an essential role in carboxysome assembly and Rubisco encapsulation. Its mechanism of action, however, is not fully understood. Here we synthetically engineer α-carboxysome shells using minimal shell components and determine cryoEM structures of these to decipher the principle of shell assembly and encapsulation. The structures reveal that the intrinsically disordered CsoS2 C-terminus is well-structured and acts as a universal "molecular thread" stitching through multiple shell protein interfaces. We further uncover in CsoS2 a highly conserved repetitive key interaction motif, [IV]TG, which is critical to the shell assembly and architecture. Our study provides a general mechanism for the CsoS2-governed carboxysome shell assembly and cargo encapsulation and further advances synthetic engineering of carboxysomes for diverse biotechnological applications.
History
DepositionSep 4, 2022-
Header (metadata) releaseAug 23, 2023-
Map releaseAug 23, 2023-
UpdateSep 20, 2023-
Current statusSep 20, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15720.png

Downloads & links

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Map

FileDownload / File: emd_15720.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 600 pix.
= 498.6 Å		0.83 Å/pix.
x 600 pix.
= 498.6 Å		0.83 Å/pix.
x 600 pix.
= 498.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.042258162 - 0.1683994
Average (Standard dev.)0.0011670499 (±0.01364253)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 498.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half1 map

Fileemd_15720_half_map_1.map
Annotationhalf1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half2 map

Fileemd_15720_half_map_2.map
Annotationhalf2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mini-shell assembly from Halothiobacillus neapolitanus in icosahe...

EntireName: mini-shell assembly from Halothiobacillus neapolitanus in icosahedral form
Components
  • Complex: mini-shell assembly from Halothiobacillus neapolitanus in icosahedral form

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Supramolecule #1: mini-shell assembly from Halothiobacillus neapolitanus in icosahe...

SupramoleculeName: mini-shell assembly from Halothiobacillus neapolitanus in icosahedral form
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)

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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: 8.1
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 7871
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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