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- EMDB-14381: Cryo-EM structure of the Cyanobium sp. PCC 7001 Carboxysome inter... -

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Basic information

Entry
Database: EMDB / ID: EMD-14381
TitleCryo-EM structure of the Cyanobium sp. PCC 7001 Carboxysome internal density middle layer
Map dataCryo-EM structure of the Cyanobium sp. PCC 7001 Carboxysome internal density middle layer
Sample
  • Organelle or cellular component: Carboxysome
KeywordsCarboxysome / Carbon Fixation / Cyanobacteria / PHOTOSYNTHESIS
Biological speciesCyanobium sp. PCC 7001 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsEvans SL / Mann D / Bergeron JRC
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Structure / Year: 2023
Title: Single-particle cryo-EM analysis of the shell architecture and internal organization of an intact α-carboxysome.
Authors: Sasha L Evans / Monsour M J Al-Hazeem / Daniel Mann / Nicolas Smetacek / Andrew J Beavil / Yaqi Sun / Taiyu Chen / Gregory F Dykes / Lu-Ning Liu / Julien R C Bergeron /
Abstract: Carboxysomes are proteinaceous bacterial microcompartments that sequester the key enzymes for carbon fixation in cyanobacteria and some proteobacteria. They consist of a virus-like icosahedral shell, ...Carboxysomes are proteinaceous bacterial microcompartments that sequester the key enzymes for carbon fixation in cyanobacteria and some proteobacteria. They consist of a virus-like icosahedral shell, encapsulating several enzymes, including ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), responsible for the first step of the Calvin-Benson-Bassham cycle. Despite their significance in carbon fixation and great bioengineering potentials, the structural understanding of native carboxysomes is currently limited to low-resolution studies. Here, we report the characterization of a native α-carboxysome from a marine cyanobacterium by single-particle cryoelectron microscopy (cryo-EM). We have determined the structure of its RuBisCO enzyme, and obtained low-resolution maps of its icosahedral shell, and of its concentric interior organization. Using integrative modeling approaches, we have proposed a complete atomic model of an intact carboxysome, providing insight into its organization and assembly. This is critical for a better understanding of the carbon fixation mechanism and toward repurposing carboxysomes in synthetic biology for biotechnological applications.
History
DepositionFeb 18, 2022-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateJun 14, 2023-
Current statusJun 14, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14381.png

Downloads & links

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Map

FileDownload / File: emd_14381.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the Cyanobium sp. PCC 7001 Carboxysome internal density middle layer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 128 pix.
= 142.08 Å		1.11 Å/pix.
x 128 pix.
= 142.08 Å		1.11 Å/pix.
x 128 pix.
= 142.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.1
Minimum - Maximum-3.6904852 - 4.4975123
Average (Standard dev.)0.018860348 (±0.23474772)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 142.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Carboxysome

EntireName: Carboxysome
Components
  • Organelle or cellular component: Carboxysome

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Supramolecule #1: Carboxysome

SupramoleculeName: Carboxysome / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Cyanobium sp. PCC 7001 (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
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: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3533
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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