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- EMDB-37730: Cryo-ET map of RuBisCO at the outermost layer that is loosely att... -

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Basic information

Entry
Database: EMDB / ID: EMD-37730
TitleCryo-ET map of RuBisCO at the outermost layer that is loosely attached to the shell of Synechococcus elongatus PCC 7942 beta-carboxysome
Map data
Sample
  • Complex: RuBisCO(type3)
Keywordscarboxysome / RuBisCO / cryo-et / PHOTOSYNTHESIS
Biological speciesSynechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805) (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 8.4 Å
AuthorsKong WW / Jiang YL / Zhou CZ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32241025 China
CitationJournal: Structure / Year: 2024
Title: Cryo-electron tomography reveals the packaging pattern of RuBisCOs in Synechococcus β-carboxysome.
Authors: Wen-Wen Kong / Yun Zhu / Heng-Rui Zhao / Kang Du / Rui-Qian Zhou / Bo Li / Feng Yang / Pu Hou / Xia-He Huang / Yuxing Chen / Ying-Chun Wang / Fei Sun / Yong-Liang Jiang / Cong-Zhao Zhou /
Abstract: Carboxysomes are large self-assembled microcompartments that serve as the central machinery of a CO-concentrating mechanism (CCM). Biogenesis of carboxysome requires the fine organization of ...Carboxysomes are large self-assembled microcompartments that serve as the central machinery of a CO-concentrating mechanism (CCM). Biogenesis of carboxysome requires the fine organization of thousands of individual proteins; however, the packaging pattern of internal RuBisCOs remains largely unknown. Here we purified the intact β-carboxysomes from Synechococcus elongatus PCC 7942 and identified the protein components by mass spectrometry. Cryo-electron tomography combined with subtomogram averaging revealed the general organization pattern of internal RuBisCOs, in which the adjacent RuBisCOs are mainly arranged in three distinct manners: head-to-head, head-to-side, and side-by-side. The RuBisCOs in the outermost layer are regularly aligned along the shell, the majority of which directly interact with the shell. Moreover, statistical analysis enabled us to propose an ideal packaging model of RuBisCOs in the β-carboxysome. These results provide new insights into the biogenesis of β-carboxysomes and also advance our understanding of the efficient carbon fixation functionality of carboxysomes.
History
DepositionOct 10, 2023-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37730.png

Downloads & links

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Map

FileDownload / File: emd_37730.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.72 Å/pix.
x 96 pix.
= 261.12 Å		2.72 Å/pix.
x 96 pix.
= 261.12 Å		2.72 Å/pix.
x 96 pix.
= 261.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00848
Minimum - Maximum-0.018117458 - 0.022339208
Average (Standard dev.)0.0012545028 (±0.0029693379)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 261.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37730_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37730_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RuBisCO(type3)

EntireName: RuBisCO(type3)
Components
  • Complex: RuBisCO(type3)

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Supramolecule #1: RuBisCO(type3)

SupramoleculeName: RuBisCO(type3) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805) (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 300 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / 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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number subtomograms used: 2300
ExtractionNumber tomograms: 88 / Number images used: 53000
Final angle assignmentType: RANDOM ASSIGNMENT

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