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- EMDB-15801: cryo-EM structure of carboxysomal mini-shell: icosahedral assembl... -

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Basic information

Entry
Database: EMDB / ID: EMD-15801
Titlecryo-EM structure of carboxysomal mini-shell: icosahedral assembly from CsoS4A/1A and CsoS2 co-expression (T = 9)
Map datamain map
Sample
  • Complex: mini-shell assembly from Halothiobacillus neapolitanus with CsoS4A/1A and CsoS2 co-expression (T= 9)
    • Protein or peptide: Major carboxysome shell protein CsoS1A
    • Protein or peptide: Carboxysome shell vertex protein CsoS4A
    • Protein or peptide: Carboxysome assembly protein CsoS2B
  • 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 assembly protein / Carboxysome shell peptide mid-region / Carboxysome shell vertex protein CsoS4A / Bacterial microcompartment vertex (BMV) domain profile. / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / CcmK/CsoS1, bacterial microcompartment domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. ...Carboxysome assembly protein / Carboxysome shell peptide mid-region / Carboxysome shell vertex protein CsoS4A / Bacterial microcompartment vertex (BMV) domain profile. / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / CcmK/CsoS1, bacterial microcompartment domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC
Similarity search - Domain/homology
Carboxysome assembly protein CsoS2B / Carboxysome shell vertex protein CsoS4A / Major carboxysome shell protein CsoS1A
Similarity search - Component
Biological speciesHalothiobacillus neapolitanus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.86 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 9, 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_15801.png

Downloads & links

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Map

FileDownload / File: emd_15801.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 720 pix.
= 598.32 Å		0.83 Å/pix.
x 720 pix.
= 598.32 Å		0.83 Å/pix.
x 720 pix.
= 598.32 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: 0.0441
Minimum - Maximum-0.16872732 - 0.30014935
Average (Standard dev.)-0.00000087009295 (±0.011585039)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 598.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15801_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_15801_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_15801_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 : mini-shell assembly from Halothiobacillus neapolitanus with CsoS4...

EntireName: mini-shell assembly from Halothiobacillus neapolitanus with CsoS4A/1A and CsoS2 co-expression (T= 9)
Components
  • Complex: mini-shell assembly from Halothiobacillus neapolitanus with CsoS4A/1A and CsoS2 co-expression (T= 9)
    • Protein or peptide: Major carboxysome shell protein CsoS1A
    • Protein or peptide: Carboxysome shell vertex protein CsoS4A
    • Protein or peptide: Carboxysome assembly protein CsoS2B
  • 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= 9)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)

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Macromolecule #1: Major carboxysome shell protein CsoS1A

MacromoleculeName: Major carboxysome shell protein CsoS1A / type: protein_or_peptide / ID: 1 / Number of copies: 8 / 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 #2: Carboxysome shell vertex protein CsoS4A

MacromoleculeName: Carboxysome shell vertex protein CsoS4A / type: protein_or_peptide / ID: 2 / 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 #3: Carboxysome assembly protein CsoS2B

MacromoleculeName: Carboxysome assembly protein CsoS2B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria) / Strain: ATCC 23641 / c2
Molecular weightTheoretical: 91.502031 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNPADLSGLS GKELARARRA ALSKQGKAAV SNKTASVNRS TKQAASSINT NQVRSSVNEV PTDYQMADQL CSTIDHADFG TESNRVRDL CRQRREALST IGKKAVKTNG KPSGRVRPQQ SVVHNDAMIE NAGDTNQSSS TSLNNELSEI CSIADDMPER F GSQAKTVR ...String:
MNPADLSGLS GKELARARRA ALSKQGKAAV SNKTASVNRS TKQAASSINT NQVRSSVNEV PTDYQMADQL CSTIDHADFG TESNRVRDL CRQRREALST IGKKAVKTNG KPSGRVRPQQ SVVHNDAMIE NAGDTNQSSS TSLNNELSEI CSIADDMPER F GSQAKTVR DICRARRQAL SERGTRAVPP KPQSQGGPGR NGYQIDGYLD TALHGRDAAK RHREMLCQYG RGTAPSCKPT GR VKNSVQS GNAAPKKVET GHTLSGGSVT GTQVDRKSHV TGNEPGTCRA VTGTEYVGTE QFTSFCNTSP KPNATKVNVT TTA RGRPVS GTEVSRTEKV TGNESGVCRN VTGTEYMSNE AHFSLCGTAA KPSQADKVMF GATARTHQVV SGSDEFRPSS VTGN ESGAK RTITGSQYAD EGLARLTING APAKVARTHT FAGSDVTGTE IGRSTRVTGD ESGSCRSISG TEYLSNEQFQ SFCDT KPQR SPFKVGQDRT NKGQSVTGNL VDRSELVTGN EPGSCSRVTG SQYGQSKICG GGVGKVRSMR TLRGTSVSGQ QLDHAP KMS GDERGGCMPV TGNEYYGREH FEPFCTSTPE PEAQSTEQSL TCEGQIISGT SVDASDLVTG NEIGEQQLIS GDAYVGA QQ TGCLPTSPRF NQTGNVQSMG FKNTNQPEQN FAPGEVMPTD FSIQTPARSA QNRITGNDIA PSGRITGPGM LATGLITG T PEFRHAAREL VGSPQPMAMA MANRNKAAQA PVVQPEVVAT QEKPELVCAP RSDQMDRVSG EGKERCHITG DDWSVNKHI TGTAGQWASG RNPSMRGNAR VVETSAFANR NVPKPEKPGS KITGSSGNDT QGSLITYSGG ARG

UniProtKB: Carboxysome assembly protein CsoS2B

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 485 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 44.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 123500
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-8b12:
cryo-EM structure of carboxysomal mini-shell: icosahedral assembly from CsoS4A/1A and CsoS2 co-expression (T = 9)

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