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- EMDB-50836: Rubisco in native beta-carboxysomes -

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Basic information

Entry
Database: EMDB / ID: EMD-50836
TitleRubisco in native beta-carboxysomes
Map dataMap of beta-carboxosome RuBisCO with SSUL density.
Sample
  • Complex: complex of Rubisco abd CcmM Small-subunit-like domain in lumens of purified beta-carboxysomes
    • Protein or peptide: Carboxysome assembly protein CcmM
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Protein or peptide: Ribulose bisphosphate carboxylase small subunit
KeywordsRubisco / CcmM / PHOTOSYNTHESIS
Function / homology
Function and homology information


structural constituent of carboxysome shell / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / carbon fixation / reductive pentose-phosphate cycle / photosynthesis / monooxygenase activity / magnesium ion binding
Similarity search - Function
Carboxysome assembly protein CcmM / : / : / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site ...Carboxysome assembly protein CcmM / : / : / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase small subunit / Carboxysome assembly protein CcmM / Ribulose bisphosphate carboxylase large chain
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 3.5 Å
AuthorsSheng Y / Hardenbrook N / Li K
Funding support United Kingdom, European Union, China, 9 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V009729/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S003339/1 United Kingdom
Royal SocietyURFR180030 United Kingdom
Royal SocietyRGFEA181061 United Kingdom
Leverhulme TrustRPG-2021-286 United Kingdom
Leverhulme TrustRPG-2019-300 United Kingdom
European Research Council (ERC)101021133European Union
Wellcome Trust206422/Z/17/Z United Kingdom
National Natural Science Foundation of China (NSFC)32070109 China
CitationJournal: Plant Physiol / Year: 2024
Title: Rubisco packaging and stoichiometric composition of the native β-carboxysome in Synechococcus elongatus PCC7942.
Authors: Yaqi Sun / Yuewen Sheng / Tao Ni / Xingwu Ge / Joscelyn Sarsby / Philip J Brownridge / Kang Li / Nathan Hardenbrook / Gregory F Dykes / Nichola Rockliffe / Claire E Eyers / Peijun Zhang / Lu-Ning Liu /
Abstract: Carboxysomes are anabolic bacterial microcompartments that play an essential role in CO2 fixation in cyanobacteria. This self-assembling proteinaceous organelle uses a polyhedral shell constructed by ...Carboxysomes are anabolic bacterial microcompartments that play an essential role in CO2 fixation in cyanobacteria. This self-assembling proteinaceous organelle uses a polyhedral shell constructed by hundreds of shell protein paralogs to encapsulate the key CO2-fixing enzymes Rubisco and carbonic anhydrase. Deciphering the precise arrangement and structural organization of Rubisco enzymes within carboxysomes is crucial for understanding carboxysome formation and overall functionality. Here, we employed cryoelectron tomography and subtomogram averaging to delineate the 3D packaging of Rubiscos within β-carboxysomes in the freshwater cyanobacterium Synechococcus elongatus PCC7942 grown under low light. Our results revealed that Rubiscos are arranged in multiple concentric layers parallel to the shell within the β-carboxysome lumen. We also detected Rubisco binding with the scaffolding protein CcmM in β-carboxysomes, which is instrumental for Rubisco encapsulation and β-carboxysome assembly. Using Quantification conCATamer-based quantitative MS, we determined the absolute stoichiometric composition of the entire β-carboxysome. This study provides insights into the assembly principles and structural variation of β-carboxysomes, which will aid in the rational design and repurposing of carboxysome nanostructures for diverse bioengineering applications.
History
DepositionJul 1, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50836.png

Downloads & links

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Map

FileDownload / File: emd_50836.map.gz / Format: CCP4 / Size: 32.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of beta-carboxosome RuBisCO with SSUL density.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 204 pix.
= 275.4 Å		1.35 Å/pix.
x 204 pix.
= 275.4 Å		1.35 Å/pix.
x 204 pix.
= 275.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.311
Minimum - Maximum-3.571484 - 4.743649
Average (Standard dev.)0.0034183688 (±0.22713561)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions204204204
Spacing204204204
CellA=B=C: 275.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map of the RuBisCo2

Fileemd_50836_half_map_1.map
AnnotationHalf-map of the RuBisCo2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map of the RuBisCo

Fileemd_50836_half_map_2.map
AnnotationHalf-map of the RuBisCo
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : complex of Rubisco abd CcmM Small-subunit-like domain in lumens o...

EntireName: complex of Rubisco abd CcmM Small-subunit-like domain in lumens of purified beta-carboxysomes
Components
  • Complex: complex of Rubisco abd CcmM Small-subunit-like domain in lumens of purified beta-carboxysomes
    • Protein or peptide: Carboxysome assembly protein CcmM
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Protein or peptide: Ribulose bisphosphate carboxylase small subunit

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Supramolecule #1: complex of Rubisco abd CcmM Small-subunit-like domain in lumens o...

SupramoleculeName: complex of Rubisco abd CcmM Small-subunit-like domain in lumens of purified beta-carboxysomes
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)

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Macromolecule #1: Carboxysome assembly protein CcmM

MacromoleculeName: Carboxysome assembly protein CcmM / type: protein_or_peptide / ID: 1
Details: LSSEVITQVRSLLNQGYRIGTEHADKRRFRTSSWQPCAPIQSTNERQVLSELENCLSEHEGEYVRLLGIDTNTRSRVFEALIQRPD
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Molecular weightTheoretical: 9.944059 KDa
SequenceString:
LSSEVITQVR SLLNQGYRIG TEHADKRRFR TSSWQPCAPI QSTNERQVLS ELENCLSEHE GEYVRLLGID TNTRSRVFEA LIQRPD

UniProtKB: Carboxysome assembly protein CcmM

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Macromolecule #2: Ribulose bisphosphate carboxylase large chain

MacromoleculeName: Ribulose bisphosphate carboxylase large chain / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Molecular weightTheoretical: 49.05059 KDa
SequenceString: YKLTYYTPDY TPKDTDLLAA FRFSPQPGVP ADEAGAAIAA ESSTGTWTTV WTDLLTDMDR YKGKCYHIEP VQGEENSYFA FIAYPLDLF EEGSVTNILT SIVGNVFGFK AIRSLRLEDI RFPVALVKTF QGPPHGIQVE RDLLNKYGRP MLGCTIKPKL G LSAKNYGR ...String:
YKLTYYTPDY TPKDTDLLAA FRFSPQPGVP ADEAGAAIAA ESSTGTWTTV WTDLLTDMDR YKGKCYHIEP VQGEENSYFA FIAYPLDLF EEGSVTNILT SIVGNVFGFK AIRSLRLEDI RFPVALVKTF QGPPHGIQVE RDLLNKYGRP MLGCTIKPKL G LSAKNYGR AVYECLRGGL DFTKDDENIN SQPFQRWRDR FLFVADAIHK SQAETGEIKG HYLNVTAPTC EEMMKRAEFA KE LGMPIIM HDFLTAGFTA NTTLAKWCRD NGVLLHIHRA MHAVIDRQRN HGIHFRVLAK CLRLSGGDHL HSGTVVGKLE GDK ASTLGF VDLMREDHIE ADRSRGVFFT QDWASMPGVL PVASGGIHVW HMPALVEIFG DDSVLQFGGG TLGHPWGNAP GATA NRVAL EACVQARNEG RDLYREGGDI LREAGKWSPE LAAALDL

UniProtKB: Ribulose bisphosphate carboxylase large chain

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Macromolecule #3: Ribulose bisphosphate carboxylase small subunit

MacromoleculeName: Ribulose bisphosphate carboxylase small subunit / type: protein_or_peptide / ID: 3 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Molecular weightTheoretical: 12.181751 KDa
SequenceString:
KERRFETFSY LPPLSDRQIA AQIEYMIEQG FHPLIEFNEH SNPEEFYWTM WKLPLFDCKS PQQVLDEVRE CRSEYGDCYI RVAGFDNIK QCQTVSFIVH RP

UniProtKB: Ribulose bisphosphate carboxylase small subunit

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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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.5 µm / Nominal defocus min: 2.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 185
ExtractionNumber tomograms: 65 / Number images used: 185
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: OTHER / Software - Name: emClarity / Details: Cross correlation

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