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- EMDB-14592: Subtomogram averaging of Rubiscos along the shell of Halothiobaci... -

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Basic information

Entry
Database: EMDB / ID: EMD-14592
TitleSubtomogram averaging of Rubiscos along the shell of Halothiobacillus carboxysome
Map dataemClarity combined map from cisTEM reconstruction, postprocessed by relion
Sample
  • Complex: alpha carboxysomes
    • 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 speciesHalothiobacillus neapolitanus (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 3.82 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 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_14592.png

Downloads & links

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Map

FileDownload / File: emd_14592.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationemClarity combined map from cisTEM reconstruction, postprocessed by relion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 200 pix.
= 268. Å		1.34 Å/pix.
x 200 pix.
= 268. Å		1.34 Å/pix.
x 200 pix.
= 268. 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: 0.318
Minimum - Maximum-3.3379147 - 4.6976795
Average (Standard dev.)0.017540285 (±0.24468006)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 268.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: emClarity half map 1 from cisTEM reconstruction

Fileemd_14592_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_14592_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 : alpha carboxysomes

EntireName: alpha carboxysomes
Components
  • Complex: alpha carboxysomes
    • 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: alpha carboxysomes

SupramoleculeName: alpha carboxysomes / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Halothiobacillus neapolitanus (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: Halothiobacillus neapolitanus (bacteria)
SequenceString: MAVKKYSAGV KEYRQTYWMP EYTPLDSDIL ACFKITPQPG VDREEAAAAV AAESSTGTWT TVWTDLLTD MDYYKGRAYR IEDVPGDDAA FYAFIAYPID LFEEGSVVNV FTSLVGNVFG F KAVRGLRL EDVRFPLAYV KTCGGPPHGI QVERDKMNKY GRPLLGCTIK ...String:
MAVKKYSAGV KEYRQTYWMP EYTPLDSDIL ACFKITPQPG VDREEAAAAV AAESSTGTWT TVWTDLLTD MDYYKGRAYR IEDVPGDDAA FYAFIAYPID LFEEGSVVNV FTSLVGNVFG F KAVRGLRL EDVRFPLAYV KTCGGPPHGI QVERDKMNKY GRPLLGCTIK PKLGLSAKNY GR AVYECLR GGLDFTKDDE NINSQPFMRW RDRFLFVQDA TETAEAQTGE RKGHYLNVTA PTP EEMYKR AEFAKEIGAP IIMHDYITGG FTANTGLAKW CQDNGVLLHI HRAMHAVIDR NPNH GIHFR VLTKILRLSG GDHLHTGTVV GKLEGDRAST LGWIDLLRES FIPEDRSRGI FFDQD WGSM PGVFAVASGG IHVWHMPALV NIFGDDSVLQ FGGGTLGHPW GNAAGAAANR VALEAC VEA RNQGRDIEKE GKEILTAAAQ HSPELKIAME TWKEIKFEFD TVDKLDTQNR

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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: Halothiobacillus neapolitanus (bacteria)
SequenceString:
MAEMQDYKQS LKYETFSYLP PMNAERIRAQ IKYAIAQGWS PGIEHVEVKN SMNQYWYMWK LPFFGEQNV DNVLAEIEAC RSAYPTHQVK LVAYDNYAQS LGLAFVVYRG N

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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) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: emClarity, cisTEM) / Number subtomograms used: 55705
ExtractionNumber tomograms: 60 / Number images used: 55705 / Software - Name: emClarity
Final 3D classificationNumber classes: 1
Final angle assignmentType: OTHER / Software - Name: emClarity / Details: cross correlation

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Atomic model buiding 1

Initial modelPDB ID:

6uew

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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