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- EMDB-38544: Cryo-EM map of the intact shell of alpha-carboxysome from Prochlo... -

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Basic information

Entry
Database: EMDB / ID: EMD-38544
TitleCryo-EM map of the intact shell of alpha-carboxysome from Prochlorococcus MED4
Map data
Sample
  • Complex: alpha-carboxysome shell
    • Protein or peptide: the shell hexamer CsoS1
    • Protein or peptide: The shell pentamer CsoS4A
    • Protein or peptide: The scaffolding protein CsoS2
Keywordsalpha-carboxysome / carbon fixation / PHOTOSYNTHESIS
Biological speciesProchlorococcus sp. MED4 (bacteria) / Prochlorococcus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 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_38544.png

Downloads & links

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Map

FileDownload / File: emd_38544.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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.011752326 - 0.021285366
Average (Standard dev.)0.00023267725 (±0.0013049812)
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_38544_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_38544_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 : alpha-carboxysome shell

EntireName: alpha-carboxysome shell
Components
  • Complex: alpha-carboxysome shell
    • Protein or peptide: the shell hexamer CsoS1
    • Protein or peptide: The shell pentamer CsoS4A
    • Protein or peptide: The scaffolding protein CsoS2

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Supramolecule #1: alpha-carboxysome shell

SupramoleculeName: alpha-carboxysome shell / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Prochlorococcus sp. MED4 (bacteria)
Molecular weightTheoretical: 39.6 MDa

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Macromolecule #1: the shell hexamer CsoS1

MacromoleculeName: the shell hexamer CsoS1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString:
MGIALGMIET RGLVPAIEAA DAMTKAAEVR LIGREFVGGG YVTVLVRGET GAVNA AVRA GADACERVGD GLVAAHIIAR PHREVEPALG NGDFLGQKD

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Macromolecule #2: The shell pentamer CsoS4A

MacromoleculeName: The shell pentamer CsoS4A / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Prochlorococcus (bacteria)
SequenceString:
MLICKVLKPL VSTNRIPGFE HKHLQVVLDG SSNKVAVDAV GCKPGDWVIC VGSSAAREAA GSKSYPSDL TIVGIIDHWD PDSPKQIEV

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Macromolecule #3: The scaffolding protein CsoS2

MacromoleculeName: The scaffolding protein CsoS2 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Prochlorococcus (bacteria)
SequenceString: MSTKTSREIA LERRKAMSDG GKKAALHSSS TKDRVRSSQD INSTGATSSN KKVLTSPSKS NIPANKIAR KSTSSKLSSK ELGIERRKAM STHGKSAINS SDRTRTDVKS DIKVNKVIST E KPQALKDH NNNIKDNQVV KQNIKRRINQ KRKPITNTSR DIVLARREAQ ...String:
MSTKTSREIA LERRKAMSDG GKKAALHSSS TKDRVRSSQD INSTGATSSN KKVLTSPSKS NIPANKIAR KSTSSKLSSK ELGIERRKAM STHGKSAINS SDRTRTDVKS DIKVNKVIST E KPQALKDH NNNIKDNQVV KQNIKRRINQ KRKPITNTSR DIVLARREAQ SKHGKSASKQ NT SAASLAR RGDPDLSSRE ISQRVRELRS KTGSTSKQGN GKCRPCGPNK NGSKLNIADA SWK VGKSET DSGQTVTGTQ ANRSLKTTGN EASTCRTVTG TQYMGAEVTG QFCQDKPKYK QPIR ASVTT TTSGNKVTGN EVGRSEKVTG DEPGTCKNLT GTEYISANQS KKYCGEVIKK PSKVM QSIT TDGLKVSGSL PGRSSLVTGD ESGSGKQLTG DQYLGSEPSP KGKSFEKVGS YDTLNG NNV TGTGVGRSDY VTGNEYGSCK NLTGDEYIGS QQYEKFCGST PKPEARKVGL SLSSKSN LI SGTMTGRSKI VTGDEPGSCK VLTGTPYAGL DQINDNCNAE IADDMKSRAT VNSGNNSN A RLTGLQPGIG GVMTGATKGS CKNLTGTPYI GGDQFLSNCE TPPNDASYAN QEKSASNSW KEFSVNSPSR EKYSAKNTEG VTGNRYEDSS KITGPFDMAE DKVTGTEQFR FEPNKNMTYK QKMKQEESQ NIDIPTDKKE PSKITGEGQS AGNITGDDWD RGDKVTGTEG VSARKRNPSR A GFMGAMPP VDNKRNDETE KPDFLITGSS GNTRDGQLVT FSGGARG

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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 / Details: alphaFold predicted model
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.3 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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