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- EMDB-30385: Simplified Alpha-Carboxysome, T=4 -

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Basic information

Entry
Database: EMDB / ID: EMD-30385
TitleSimplified Alpha-Carboxysome, T=4
Map dataSimplified Alpha-Carboxysome, T=4
Sample
  • Organelle or cellular component: Simplified Alpha-Carboxysome, T=4
    • Protein or peptide: Unidentified carboxysome polypeptide
    • Protein or peptide: Major carboxysome shell protein 1A
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation
Similarity search - Function
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 ...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 shell vertex protein CsoS4A / Major carboxysome shell protein CsoS1A
Similarity search - Component
Biological speciesHalothiobacillus neapolitanus (bacteria) / Halothiobacillus neapolitanus (strain ATCC 23641 / c2) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsTan YQ / Ali S / Xue B / Robinson RC / Narita A / Yew WS
Funding support Singapore, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore) Singapore
CitationJournal: Biomacromolecules / Year: 2021
Title: Structure of a Minimal α-Carboxysome-Derived Shell and Its Utility in Enzyme Stabilization.
Authors: Yong Quan Tan / Samson Ali / Bo Xue / Wei Zhe Teo / Lay Hiang Ling / Maybelle Kho Go / Hong Lv / Robert C Robinson / Akihiro Narita / Wen Shan Yew /
Abstract: Bacterial microcompartments are proteinaceous shells that encase specialized metabolic processes in bacteria. Recent advances in simplification of these intricate shells have encouraged ...Bacterial microcompartments are proteinaceous shells that encase specialized metabolic processes in bacteria. Recent advances in simplification of these intricate shells have encouraged bioengineering efforts. Here, we construct minimal shells derived from the α-carboxysome, which we term Cso-shell. Using cryogenic electron microscopy, the atomic-level structures of two shell forms were obtained, reinforcing notions of evolutionarily conserved features in bacterial microcompartment shell architecture. Encapsulation peptide sequences that facilitate loading of heterologous protein cargo within the shells were identified. We further provide a first demonstration in utilizing minimal bacterial microcompartment-derived shells for hosting heterologous enzymes. Cso-shells were found to stabilize enzymatic activities against heat shock, presence of methanol co-solvent, consecutive freeze-thawing, and alkaline environments. This study yields insights into α-carboxysome assembly and advances the utility of synthetic bacterial microcompartments as nanoreactors capable of stabilizing enzymes with varied properties and reaction chemistries.
History
DepositionJul 16, 2020-
Header (metadata) releaseAug 25, 2021-
Map releaseAug 25, 2021-
UpdateFeb 16, 2022-
Current statusFeb 16, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ckc
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ckc
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30385.png

Downloads & links

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Map

FileDownload / File: emd_30385.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSimplified Alpha-Carboxysome, T=4
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.07536025 - 0.123255625
Average (Standard dev.)0.0015906028 (±0.011307039)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 258.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z258.000258.000258.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0750.1230.002

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Supplemental data

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Sample components

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Entire : Simplified Alpha-Carboxysome, T=4

EntireName: Simplified Alpha-Carboxysome, T=4
Components
  • Organelle or cellular component: Simplified Alpha-Carboxysome, T=4
    • Protein or peptide: Unidentified carboxysome polypeptide
    • Protein or peptide: Major carboxysome shell protein 1A

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Supramolecule #1: Simplified Alpha-Carboxysome, T=4

SupramoleculeName: Simplified Alpha-Carboxysome, T=4 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)
Molecular weightTheoretical: 2.3 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Unidentified carboxysome polypeptide

MacromoleculeName: Unidentified carboxysome polypeptide / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)
Molecular weightTheoretical: 10.17364 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKIMQVEKTL VSTNRIADMG HKPLLVVWEK PGAPRQVAVD AIGCIPGDWV LCVGSSAARE AAGSKSYPSD LTIIGIIDQW NGEGSSWSH PQFEK

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Macromolecule #2: Major carboxysome shell protein 1A

MacromoleculeName: Major carboxysome shell protein 1A / type: protein_or_peptide / ID: 2 / Number of copies: 180 / Enantiomer: LEVO
Source (natural)Organism: Halothiobacillus neapolitanus (strain ATCC 23641 / c2) (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

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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: 7.9
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K

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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
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 64.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 94129
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Software - details: CTFFIND in RELION was used
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.7) / Software - details: RELION software was used throughout / Number images used: 67192

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Atomic model buiding 1

Initial model(PDB ID:

2rcf

,

2ewh

)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7ckc:
Simplified Alpha-Carboxysome, T=4

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