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- EMDB-14590: Subtomogram averaging of Rubisco from native Halothiobacillus car... -

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Basic information

Entry
Database: EMDB / ID: EMD-14590
TitleSubtomogram averaging of Rubisco from native Halothiobacillus carboxysomes
Map datafinal merged map
Sample
  • Complex: alpha carboxysomes
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Protein or peptide: Ribulose bisphosphate carboxylase small subunit
KeywordsRubisco / carboxysome / UNKNOWN FUNCTION
Function / homology
Function and homology information


carboxysome / 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 speciesHalothiobacillus neapolitanus (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 3.3 Å
AuthorsNi T / Zhu Y / Yu X / Sun Y / Liu L / Zhang P
Funding supportEuropean Union, United Kingdom, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Wellcome Trust United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
Citation
Journal: 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.
#1: Journal: bioRxiv / Year: 2022
Title: Tales of Two alpha Carboxysomes the Structure and Assembly of Cargo Rubisco
Authors: Ni T / Sun Y / Seaton-Burn W / AI-Hazeem M / Zhu Y / Yu X / Liu L / Zhang P
History
DepositionMar 24, 2022-
Header (metadata) releaseJul 20, 2022-
Map releaseJul 20, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14590.png

Downloads & links

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Map

FileDownload / File: emd_14590.map.gz / Format: CCP4 / Size: 21.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfinal merged map
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-12.244395000000001 - 17.588619999999999
Average (Standard dev.)0.031158246 (±0.8440962)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions177177177
Spacing177177177
CellA=B=C: 237.18001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 2

Fileemd_14590_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_14590_half_map_2.map
Annotationhalf map 1
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 carboxysomes

EntireName: alpha carboxysomes
Components
  • Complex: alpha carboxysomes
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Protein or peptide: Ribulose bisphosphate carboxylase small subunit

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Supramolecule #1: alpha carboxysomes

SupramoleculeName: alpha carboxysomes / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Halothiobacillus neapolitanus (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: Halothiobacillus neapolitanus (bacteria) / Strain: ATCC 23641 / c2
Molecular weightTheoretical: 52.7025 KDa
Recombinant expressionOrganism: Halothiobacillus neapolitanus (bacteria)
SequenceString: MAVKKYSAGV KEYRQTYWMP EYTPLDSDIL ACFKITPQPG VDREEAAAAV AAESSTGTWT TVWTDLLTDM DYYKGRAYRI EDVPGDDAA FYAFIAYPID LFEEGSVVNV FTSLVGNVFG FKAVRGLRLE DVRFPLAYVK TCGGPPHGIQ VERDKMNKYG R PLLGCTIK ...String:
MAVKKYSAGV KEYRQTYWMP EYTPLDSDIL ACFKITPQPG VDREEAAAAV AAESSTGTWT TVWTDLLTDM DYYKGRAYRI EDVPGDDAA FYAFIAYPID LFEEGSVVNV FTSLVGNVFG FKAVRGLRLE DVRFPLAYVK TCGGPPHGIQ VERDKMNKYG R PLLGCTIK PKLGLSAKNY GRAVYECLRG GLDFTKDDEN INSQPFMRWR DRFLFVQDAT ETAEAQTGER KGHYLNVTAP TP EEMYKRA EFAKEIGAPI IMHDYITGGF TANTGLAKWC QDNGVLLHIH RAMHAVIDRN PNHGIHFRVL TKILRLSGGD HLH TGTVVG KLEGDRASTL GWIDLLRESF IPEDRSRGIF FDQDWGSMPG VFAVASGGIH VWHMPALVNI FGDDSVLQFG GGTL GHPWG NAAGAAANRV ALEACVEARN QGRDIEKEGK EILTAAAQHS PELKIAMETW KEIKFEFDTV DKLDTQNR

UniProtKB: Ribulose bisphosphate carboxylase large chain

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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: Halothiobacillus neapolitanus (bacteria) / Strain: ATCC 23641 / c2
Molecular weightTheoretical: 12.866575 KDa
Recombinant expressionOrganism: Halothiobacillus neapolitanus (bacteria)
SequenceString:
MAEMQDYKQS LKYETFSYLP PMNAERIRAQ IKYAIAQGWS PGIEHVEVKN SMNQYWYMWK LPFFGEQNVD NVLAEIEACR SAYPTHQVK LVAYDNYAQS LGLAFVVYRG N

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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k 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: 6.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Detailsthe raw micrographs were motioncorrected and stacked into tilt-series, aligned in etomo, the processed in emClarity
Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: emClarity / Number subtomograms used: 149479
ExtractionNumber tomograms: 60 / Number images used: 149479
Final 3D classificationNumber classes: 1
Final angle assignmentType: OTHER / Software - Name: emClarity / Details: cross correlation
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1svd


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 94.7
Output model

PDB-7zbt:
Subtomogram averaging of Rubisco from native Halothiobacillus carboxysomes

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