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- EMDB-14623: Subtomogram averaging of Rubisco from Cyanobium carboxysome (inne... -

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Basic information

Entry
Database: EMDB / ID: EMD-14623
TitleSubtomogram averaging of Rubisco from Cyanobium carboxysome (innermost layer)
Map data
Sample
  • Complex: Rubisco from Cyanobium carboxysome (innermost layer)
    • Protein or peptide: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) large subunit
    • Protein or peptide: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) small subunit
Biological speciesCyanobium sp. PCC 7001 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 4.8 Å
AuthorsNi T / Seaton-Burn W / Zhu Y / Zhang P
Funding support United Kingdom, European Union, 3 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
European Research Council (ERC)European Union
CitationJournal: Nat Commun / Year: 2022
Title: Structure and assembly of cargo Rubisco in two native α-carboxysomes.
Authors: Tao Ni / Yaqi Sun / Will Burn / Monsour M J Al-Hazeem / Yanan Zhu / Xiulian Yu / Lu-Ning Liu / Peijun Zhang /
Abstract: Carboxysomes are a family of bacterial microcompartments in cyanobacteria and chemoautotrophs. They encapsulate Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase ...Carboxysomes are a family of bacterial microcompartments in cyanobacteria and chemoautotrophs. They encapsulate Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase catalyzing carbon fixation inside a proteinaceous shell. How Rubisco complexes pack within the carboxysomes is unknown. Using cryo-electron tomography, we determine the distinct 3D organization of Rubisco inside two distant α-carboxysomes from a marine α-cyanobacterium Cyanobium sp. PCC 7001 where Rubiscos are organized in three concentric layers, and from a chemoautotrophic bacterium Halothiobacillus neapolitanus where they form intertwining spirals. We further resolve the structures of native Rubisco as well as its higher-order assembly at near-atomic resolutions by subtomogram averaging. The structures surprisingly reveal that the authentic intrinsically disordered linker protein CsoS2 interacts with Rubiscos in native carboxysomes but functions distinctively in the two α-carboxysomes. In contrast to the uniform Rubisco-CsoS2 association in the Cyanobium α-carboxysome, CsoS2 binds only to the Rubiscos close to the shell in the Halo α-carboxysome. Our findings provide critical knowledge of the assembly principles of α-carboxysomes, which may aid in the rational design and repurposing of carboxysome structures for new functions.
History
DepositionMar 25, 2022-
Header (metadata) releaseJul 13, 2022-
Map releaseJul 13, 2022-
UpdateJan 18, 2023-
Current statusJan 18, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14623.png

Downloads & links

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Map

FileDownload / File: emd_14623.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 208 pix.
= 278.72 Å		1.34 Å/pix.
x 208 pix.
= 278.72 Å		1.34 Å/pix.
x 208 pix.
= 278.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-3.549111 - 5.0522027
Average (Standard dev.)-0.006945795 (±0.2236498)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 278.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14623_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: emClarity half map 1 from cisTEM reconstruction

Fileemd_14623_half_map_1.map
AnnotationemClarity half map 1 from cisTEM reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: emClarity half map 2 from cisTEM reconstruction

Fileemd_14623_half_map_2.map
AnnotationemClarity half map 2 from cisTEM reconstruction
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 from Cyanobium carboxysome (innermost layer)

EntireName: Rubisco from Cyanobium carboxysome (innermost layer)
Components
  • Complex: Rubisco from Cyanobium carboxysome (innermost layer)
    • Protein or peptide: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) large subunit
    • Protein or peptide: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) small subunit

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Supramolecule #1: Rubisco from Cyanobium carboxysome (innermost layer)

SupramoleculeName: Rubisco from Cyanobium carboxysome (innermost layer) / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Cyanobium sp. PCC 7001 (bacteria)

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Macromolecule #1: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) large s...

MacromoleculeName: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) large subunit
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Cyanobium sp. PCC 7001 (bacteria)
SequenceString: MSKKYDAGVK EYRDTYWTPD YVPLDTDLLA CFKCTGQEGV PKEEVAAAVA AESSTGTWST VWSELLVDL DFYKGRCYRI EDVPGDKEAF YAFIAYPLDL FEEGSVTNVL TSLVGNVFGF K ALRHLRLE DIRFPMAFIK TCPGPPNGIC VERDRMNKYG RPLLGCTIKP ...String:
MSKKYDAGVK EYRDTYWTPD YVPLDTDLLA CFKCTGQEGV PKEEVAAAVA AESSTGTWST VWSELLVDL DFYKGRCYRI EDVPGDKEAF YAFIAYPLDL FEEGSVTNVL TSLVGNVFGF K ALRHLRLE DIRFPMAFIK TCPGPPNGIC VERDRMNKYG RPLLGCTIKP KLGLSGKNYG RV VYECLRG GLDFTKDDEN INSQPFQRWQ NRFEFVAEAV ALAQQETGEK KGHYLNCTAA TPE EMYERA EFAKELGQPI IMHDYITGGF TANTGLSKWC RKNGMLLHIH RAMHAVIDRH PKHG IHFRV LAKCLRLSGG DQLHTGTVVG KLEGDRQTTL GFIDQLRESF IPEDRSRGNF FDQDW GSMP GVFAVASGGI HVWHMPALVA IFGDDSVLQF GGGTHGHPWG SAAGAAANRV ALEACV KAR NAGREIEKES RDILMEAAKH SPELAIALET WKEIKFEFDT VDKLDVQ

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Macromolecule #2: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) small s...

MacromoleculeName: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) small subunit
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Cyanobium sp. PCC 7001 (bacteria)
SequenceString:
MPFKSTVGDY QTVATLETFG FLPPMTQDEI YDQIAYIIAQ GWSPLIEHVH PSRSMATYWS YWKLPFFGE KDLGVIVSEL EACHRAYPDH HVRLVGYDAY TQSQGACFVV FEGR

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.65 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 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) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: emClarity, cisTEM) / Number subtomograms used: 21650
ExtractionNumber tomograms: 139 / Number images used: 21650
Final angle assignmentType: OTHER / Software - Name: emClarity / Details: cross correlation
FSC plot (resolution estimation)

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