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- EMDB-37729: Cryo-ET map of RuBisCO-SSUL at 5.9 angstroms from Synechococcus e... -

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Basic information

Entry
Database: EMDB / ID: EMD-37729
TitleCryo-ET map of RuBisCO-SSUL at 5.9 angstroms from Synechococcus elongatus PCC 7942 beta-carboxysome
Map data
Sample
  • Complex: RuBisCO-SSUL
Keywordscarboxysome / RuBisCO / cryo-et / PHOTOSYNTHESIS
Biological speciesSynechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805) (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 5.9 Å
AuthorsKong WW / Jiang YL / Zhou CZ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32241025 China
CitationJournal: To Be Published
Title: Cryo-electron tomography reveals the packaging pattern of RuBisCOs in Synechococcus beta-carboxysome
Authors: Kong WW / Zhu Y / Zhao HR / Du K / Zhou RQ / Li B / Yang F / Hou P / Chen Y / Sun F / Jiang YL / Zhou CZ
History
DepositionOct 10, 2023-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37729.png

Downloads & links

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Map

FileDownload / File: emd_37729.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.00419
Minimum - Maximum-0.014940158 - 0.02436914
Average (Standard dev.)0.00013274641 (±0.001675913)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37729_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_37729_half_map_2.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 : RuBisCO-SSUL

EntireName: RuBisCO-SSUL
Components
  • Complex: RuBisCO-SSUL

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Supramolecule #1: RuBisCO-SSUL

SupramoleculeName: RuBisCO-SSUL / 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / 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: 3.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 88 / Number images used: 83000
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number subtomograms used: 3600

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