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- EMDB-15799: cryo-EM structure of carboxysomal mini-shell: icosahedral assembl... -

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Basic information

Entry
Database: EMDB / ID: EMD-15799
Titlecryo-EM structure of carboxysomal mini-shell: icosahedral assembly from CsoS4A/1A and CsoS2 co-expression (T = 4)
Map datamerged map
Sample
  • Complex: mini-shell assembly from Halothiobacillus neapolitanus with CsoS4A/1A and CsoS2 co-expression (T= 4)
    • Protein or peptide: Carboxysome shell vertex protein CsoS4A
    • Protein or peptide: Major carboxysome shell protein CsoS1A
  • Ligand: water
Keywordscarboxysome / shell / icosahedral symmetry / STRUCTURAL PROTEIN
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation
Similarity search - Function
Carboxysome shell vertex protein CsoS4A / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / Bacterial microcompartment vertex (BMV) domain profile. / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. ...Carboxysome shell vertex protein CsoS4A / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / Bacterial microcompartment vertex (BMV) domain profile. / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily
Similarity search - Domain/homology
Carboxysome shell vertex protein CsoS4A / Major carboxysome shell protein CsoS1A
Similarity search - Component
Biological speciesHalothiobacillus neapolitanus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsNi T / Jiang Q / Liu LN / Zhang P
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Intrinsically disordered CsoS2 acts as a general molecular thread for α-carboxysome shell assembly.
Authors: Tao Ni / Qiuyao Jiang / Pei Cing Ng / Juan Shen / Hao Dou / Yanan Zhu / Julika Radecke / Gregory F Dykes / Fang Huang / Lu-Ning Liu / Peijun Zhang /
Abstract: Carboxysomes are a paradigm of self-assembling proteinaceous organelles found in nature, offering compartmentalisation of enzymes and pathways to enhance carbon fixation. In α-carboxysomes, the ...Carboxysomes are a paradigm of self-assembling proteinaceous organelles found in nature, offering compartmentalisation of enzymes and pathways to enhance carbon fixation. In α-carboxysomes, the disordered linker protein CsoS2 plays an essential role in carboxysome assembly and Rubisco encapsulation. Its mechanism of action, however, is not fully understood. Here we synthetically engineer α-carboxysome shells using minimal shell components and determine cryoEM structures of these to decipher the principle of shell assembly and encapsulation. The structures reveal that the intrinsically disordered CsoS2 C-terminus is well-structured and acts as a universal "molecular thread" stitching through multiple shell protein interfaces. We further uncover in CsoS2 a highly conserved repetitive key interaction motif, [IV]TG, which is critical to the shell assembly and architecture. Our study provides a general mechanism for the CsoS2-governed carboxysome shell assembly and cargo encapsulation and further advances synthetic engineering of carboxysomes for diverse biotechnological applications.
History
DepositionSep 8, 2022-
Header (metadata) releaseAug 23, 2023-
Map releaseAug 23, 2023-
UpdateSep 20, 2023-
Current statusSep 20, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15799.png

Downloads & links

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Map

FileDownload / File: emd_15799.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmerged map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 425.472 Å		0.83 Å/pix.
x 512 pix.
= 425.472 Å		0.83 Å/pix.
x 512 pix.
= 425.472 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.04074152 - 0.045996707
Average (Standard dev.)0.00010566744 (±0.0028303752)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 425.472 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15799_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half1

Fileemd_15799_half_map_1.map
Annotationhalf1
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: half2

Fileemd_15799_half_map_2.map
Annotationhalf2
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : mini-shell assembly from Halothiobacillus neapolitanus with CsoS4...

EntireName: mini-shell assembly from Halothiobacillus neapolitanus with CsoS4A/1A and CsoS2 co-expression (T= 4)
Components
  • Complex: mini-shell assembly from Halothiobacillus neapolitanus with CsoS4A/1A and CsoS2 co-expression (T= 4)
    • Protein or peptide: Carboxysome shell vertex protein CsoS4A
    • Protein or peptide: Major carboxysome shell protein CsoS1A
  • Ligand: water

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Supramolecule #1: mini-shell assembly from Halothiobacillus neapolitanus with CsoS4...

SupramoleculeName: mini-shell assembly from Halothiobacillus neapolitanus with CsoS4A/1A and CsoS2 co-expression (T= 4)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)

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Macromolecule #1: Carboxysome shell vertex protein CsoS4A

MacromoleculeName: Carboxysome shell vertex protein CsoS4A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria) / Strain: ATCC 23641 / c2
Molecular weightTheoretical: 8.900287 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKIMQVEKTL VSTNRIADMG HKPLLVVWEK PGAPRQVAVD AIGCIPGDWV LCVGSSAARE AAGSKSYPSD LTIIGIIDQW NGE

UniProtKB: Carboxysome shell vertex protein CsoS4A

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Macromolecule #2: Major carboxysome shell protein CsoS1A

MacromoleculeName: Major carboxysome shell protein CsoS1A / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria) / Strain: ATCC 23641 / c2
Molecular weightTheoretical: 9.973478 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADVTGIALG MIETRGLVPA IEAADAMTKA AEVRLVGRQF VGGGYVTVLV RGETGAVNAA VRAGADACER VGDGLVAAHI IARVHSEVE NILPKAPQA

UniProtKB: Major carboxysome shell protein CsoS1A

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 45 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
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: 44.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 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: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13515
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

2ewh

source_name: PDB, initial_model_type: experimental model

2rcf

source_name: PDB, initial_model_type: experimental model
Output model

PDB-8b11:
cryo-EM structure of carboxysomal mini-shell: icosahedral assembly from CsoS4A/1A and CsoS2 co-expression (T = 4)

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