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- EMDB-38543: Cryo-EM map of the internal RuBisCOs in the alpha-carboxysome fro... -

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Basic information

Entry
Database: EMDB / ID: EMD-38543
TitleCryo-EM map of the internal RuBisCOs in the alpha-carboxysome from Prochlorococcus MED4
Map data
Sample
  • Complex: RuBisCO in the alpha-carboxysome
    • Protein or peptide: RuBisCO large subunit CbbL
    • Protein or peptide: RuBisCO small subunit CbbS
Keywordsalpha-carboxysome / carbon fixation / PHOTOSYNTHESIS
Biological speciesProchlorococcus sp. MED4 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.6 Å
AuthorsJiang YL / Zhou RQ / Zhou CZ / Zeng QL
Funding support China, Hong Kong, 5 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDA24020302 China
Chinese Academy of SciencesXDB37020301 China
The University Grants Committee, Research Grants Council (RGC)HKUST C6012-22GF Hong Kong
National Natural Science Foundation of China (NSFC)32241025 China
National Natural Science Foundation of China (NSFC)32171198 China
CitationJournal: Nat Plants / Year: 2024
Title: Structure and assembly of the α-carboxysome in the marine cyanobacterium Prochlorococcus.
Authors: Rui-Qian Zhou / Yong-Liang Jiang / Haofu Li / Pu Hou / Wen-Wen Kong / Jia-Xin Deng / Yuxing Chen / Cong-Zhao Zhou / Qinglu Zeng /
Abstract: Carboxysomes are bacterial microcompartments that encapsulate the enzymes RuBisCO and carbonic anhydrase in a proteinaceous shell to enhance the efficiency of photosynthetic carbon fixation. The self- ...Carboxysomes are bacterial microcompartments that encapsulate the enzymes RuBisCO and carbonic anhydrase in a proteinaceous shell to enhance the efficiency of photosynthetic carbon fixation. The self-assembly principles of the intact carboxysome remain elusive. Here we purified α-carboxysomes from Prochlorococcus and examined their intact structures using single-particle cryo-electron microscopy to solve the basic principles of their shell construction and internal RuBisCO organization. The 4.2 Å icosahedral-like shell structure reveals 24 CsoS1 hexamers on each facet and one CsoS4A pentamer at each vertex. RuBisCOs are organized into three concentric layers within the shell, consisting of 72, 32 and up to 4 RuBisCOs at the outer, middle and inner layers, respectively. We uniquely show how full-length and shorter forms of the scaffolding protein CsoS2 bind to the inner surface of the shell via repetitive motifs in the middle and C-terminal regions. Combined with previous reports, we propose a concomitant 'outside-in' assembly principle of α-carboxysomes: the inner surface of the self-assembled shell is reinforced by the middle and C-terminal motifs of the scaffolding protein, while the free N-terminal motifs cluster to recruit RuBisCO in concentric, three-layered spherical arrangements. These new insights into the coordinated assembly of α-carboxysomes may guide the rational design and repurposing of carboxysome structures for improving plant photosynthetic efficiency.
History
DepositionJan 2, 2024-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38543.png

Downloads & links

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Map

FileDownload / File: emd_38543.map.gz / Format: CCP4 / Size: 3.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 960 pix.
= 1017.6 Å		1.06 Å/pix.
x 960 pix.
= 1017.6 Å		1.06 Å/pix.
x 960 pix.
= 1017.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0022
Minimum - Maximum-0.00037582632 - 0.0030845522
Average (Standard dev.)0.00023814471 (±0.00063427765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions960960960
Spacing960960960
CellA=B=C: 1017.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38543_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_38543_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : RuBisCO in the alpha-carboxysome

EntireName: RuBisCO in the alpha-carboxysome
Components
  • Complex: RuBisCO in the alpha-carboxysome
    • Protein or peptide: RuBisCO large subunit CbbL
    • Protein or peptide: RuBisCO small subunit CbbS

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Supramolecule #1: RuBisCO in the alpha-carboxysome

SupramoleculeName: RuBisCO in the alpha-carboxysome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Prochlorococcus sp. MED4 (bacteria)
Molecular weightTheoretical: 56.6 MDa

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Macromolecule #1: RuBisCO large subunit CbbL

MacromoleculeName: RuBisCO large subunit CbbL / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MSKKYDAGVK EYRDTYWTPE YVPLDTDLLA CFKCTGQEGV PREEVAAAVA AESSTGTWST VWSELLTDL EFYKGRCYRI EDVPGDPEAF YAFIAYPLDL FEEGSITNVL TSLVGNVFGF K ALRHLRLE DIRFPIAFIK TCGGPPNGIV VERDRLNKYG RPLLGCTIKP ...String:
MSKKYDAGVK EYRDTYWTPE YVPLDTDLLA CFKCTGQEGV PREEVAAAVA AESSTGTWST VWSELLTDL EFYKGRCYRI EDVPGDPEAF YAFIAYPLDL FEEGSITNVL TSLVGNVFGF K ALRHLRLE DIRFPIAFIK TCGGPPNGIV VERDRLNKYG RPLLGCTIKP KLGLSGKNYG RV VYECLRG GLDLTKDDEN INSQPFQRWR ERFEFVAEAV KLAQQETGEV KGHYLNCTAN TPE ELYERA EFAKELDMPI IMHDYITGGF TANTGLANWC RKNGMLLHIH RAMHAVIDRH PKHG IHFRV LAKCLRLSGG DQLHTGTVVG KLEGDRQTTL GYIDNLRESF VPEDRSRGNF FDQDW GSMP GVFAVASGGI HVWHMPALLA IFGDDSCLQF GGGTHGHPWG SAAGAAANRV ALEACV KAR NAGREIEKES RDILMEAAKH SPELAIALET WKEIKFEFDT VDKLDVQG

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Macromolecule #2: RuBisCO small subunit CbbS

MacromoleculeName: RuBisCO small subunit CbbS / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
SequenceString:
MPFQSSVGDY QTVATLETFG FLPPMTQEEI YDQIAYIIAQ GWSPVIEHVH PSGSMQTYWS YWKLPFFGE KDLNLVVSEL EACHRAYPDH HVRIIGYDAY TQSQGTAFAV FQGR

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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: 8.5
Details: 10 mM Bicine, 1 mM EDTA, 10 mM MgCl2, and dissolved in natural sea water, pH 8.5, supplemented with 0.6 mM PMSF and 20 mM NaHCO3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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: OTHER
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 15.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3634
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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