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- EMDB-14617: Subtomogram averaging of Rubisco from Cyanobium carboxysome -

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Basic information

Entry
Database: EMDB / ID: EMD-14617
TitleSubtomogram averaging of Rubisco from Cyanobium carboxysome
Map datamain map from cisTEM reconstruction within emClarity package
Sample
  • Complex: Structure of Rubisco within Cyanobium carboxysome
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Protein or peptide: Ribulose bisphosphate carboxylase, small subunitRuBisCO
Function / homology
Function and homology information


carboxysome / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding
Similarity search - Function
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, 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
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase, small subunit
Similarity search - Component
Biological speciesCyanobium sp. PCC 7001 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 3.8 Å
AuthorsNi T / Zhu Y / Seaton-Burn W / 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 6, 2022-
Map releaseJul 6, 2022-
UpdateJan 18, 2023-
Current statusJan 18, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14617.png

Downloads & links

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Map

FileDownload / File: emd_14617.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map from cisTEM reconstruction within emClarity package
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: 0.485
Minimum - Maximum-3.4779363 - 4.734082
Average (Standard dev.)0.013149294 (±0.22134526)
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_14617_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 2 from cisTEM reconstruction

Fileemd_14617_half_map_1.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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Half map: emClarity half map 1 from cisTEM reconstruction

Fileemd_14617_half_map_2.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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Sample components

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Entire : Structure of Rubisco within Cyanobium carboxysome

EntireName: Structure of Rubisco within Cyanobium carboxysome
Components
  • Complex: Structure of Rubisco within Cyanobium carboxysome
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Protein or peptide: Ribulose bisphosphate carboxylase, small subunitRuBisCO

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Supramolecule #1: Structure of Rubisco within Cyanobium carboxysome

SupramoleculeName: Structure of Rubisco within Cyanobium carboxysome / 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 bisphosphate carboxylase large chain

MacromoleculeName: Ribulose bisphosphate carboxylase large chain / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase
Source (natural)Organism: Cyanobium sp. PCC 7001 (bacteria)
Molecular weightTheoretical: 52.526531 KDa
Recombinant expressionOrganism: Cyanobium sp. PCC 7001 (bacteria)
SequenceString: MSKKYDAGVK EYRDTYWTPD YVPLDTDLLA CFKCTGQEGV PKEEVAAAVA AESSTGTWST VWSELLVDLD FYKGRCYRIE DVPGDKEAF YAFIAYPLDL FEEGSVTNVL TSLVGNVFGF KALRHLRLED IRFPMAFIKT CPGPPNGICV ERDRMNKYGR P LLGCTIKP ...String:
MSKKYDAGVK EYRDTYWTPD YVPLDTDLLA CFKCTGQEGV PKEEVAAAVA AESSTGTWST VWSELLVDLD FYKGRCYRIE DVPGDKEAF YAFIAYPLDL FEEGSVTNVL TSLVGNVFGF KALRHLRLED IRFPMAFIKT CPGPPNGICV ERDRMNKYGR P LLGCTIKP KLGLSGKNYG RVVYECLRGG LDFTKDDENI NSQPFQRWQN RFEFVAEAVA LAQQETGEKK GHYLNCTAAT PE EMYERAE FAKELGQPII MHDYITGGFT ANTGLSKWCR KNGMLLHIHR AMHAVIDRHP KHGIHFRVLA KCLRLSGGDQ LHT GTVVGK LEGDRQTTLG FIDQLRESFI PEDRSRGNFF DQDWGSMPGV FAVASGGIHV WHMPALVAIF GDDSVLQFGG GTHG HPWGS AAGAAANRVA LEACVKARNA GREIEKESRD ILMEAAKHSP ELAIALETWK EIKFEFDTVD KLDVQ

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Macromolecule #2: Ribulose bisphosphate carboxylase, small subunit

MacromoleculeName: Ribulose bisphosphate carboxylase, small subunit / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Cyanobium sp. PCC 7001 (bacteria)
Molecular weightTheoretical: 12.967611 KDa
Recombinant expressionOrganism: Cyanobium sp. PCC 7001 (bacteria)
SequenceString:
MPFKSTVGDY QTVATLETFG FLPPMTQDEI YDQIAYIIAQ GWSPLIEHVH PSRSMATYWS YWKLPFFGEK DLGVIVSELE ACHRAYPDH 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.65 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 139 / Number images used: 152317
Final angle assignmentType: OTHER / Software - Name: emClarity / Details: cross correlation
Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: emClarity, cisTEM) / Number subtomograms used: 152317
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7zc1:
Subtomogram averaging of Rubisco from Cyanobium carboxysome

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