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

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Basic information

Entry
Database: PDB / ID: 7ckc
TitleSimplified Alpha-Carboxysome, T=4
Components
  • Major carboxysome shell protein 1A
  • Unidentified carboxysome polypeptide
KeywordsVIRUS LIKE PARTICLE / Bacterial Microcompartment / Alpha-carboxysome
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsTan, Y.Q. / Ali, S. / Xue, B. / Robinson, R.C. / Narita, A. / Yew, W.S.
Funding support Singapore, 1items
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, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
AA: Unidentified carboxysome polypeptide
BA: Major carboxysome shell protein 1A
CA: Major carboxysome shell protein 1A
DA: Major carboxysome shell protein 1A
AB: Unidentified carboxysome polypeptide
BB: Major carboxysome shell protein 1A
CB: Major carboxysome shell protein 1A
DB: Major carboxysome shell protein 1A
AC: Unidentified carboxysome polypeptide
BC: Major carboxysome shell protein 1A
CC: Major carboxysome shell protein 1A
DC: Major carboxysome shell protein 1A
AD: Unidentified carboxysome polypeptide
BD: Major carboxysome shell protein 1A
CD: Major carboxysome shell protein 1A
DD: Major carboxysome shell protein 1A
AE: Unidentified carboxysome polypeptide
BE: Major carboxysome shell protein 1A
CE: Major carboxysome shell protein 1A
DE: Major carboxysome shell protein 1A
AF: Unidentified carboxysome polypeptide
BF: Major carboxysome shell protein 1A
CF: Major carboxysome shell protein 1A
DF: Major carboxysome shell protein 1A
AG: Unidentified carboxysome polypeptide
BG: Major carboxysome shell protein 1A
CG: Major carboxysome shell protein 1A
DG: Major carboxysome shell protein 1A
AH: Unidentified carboxysome polypeptide
BH: Major carboxysome shell protein 1A
CH: Major carboxysome shell protein 1A
DH: Major carboxysome shell protein 1A
AI: Unidentified carboxysome polypeptide
BI: Major carboxysome shell protein 1A
CI: Major carboxysome shell protein 1A
DI: Major carboxysome shell protein 1A
AJ: Unidentified carboxysome polypeptide
BJ: Major carboxysome shell protein 1A
CJ: Major carboxysome shell protein 1A
DJ: Major carboxysome shell protein 1A
AK: Unidentified carboxysome polypeptide
BK: Major carboxysome shell protein 1A
CK: Major carboxysome shell protein 1A
DK: Major carboxysome shell protein 1A
AL: Unidentified carboxysome polypeptide
BL: Major carboxysome shell protein 1A
CL: Major carboxysome shell protein 1A
DL: Major carboxysome shell protein 1A
AM: Unidentified carboxysome polypeptide
BM: Major carboxysome shell protein 1A
CM: Major carboxysome shell protein 1A
DM: Major carboxysome shell protein 1A
AN: Unidentified carboxysome polypeptide
BN: Major carboxysome shell protein 1A
CN: Major carboxysome shell protein 1A
DN: Major carboxysome shell protein 1A
AO: Unidentified carboxysome polypeptide
BO: Major carboxysome shell protein 1A
CO: Major carboxysome shell protein 1A
DO: Major carboxysome shell protein 1A
AP: Unidentified carboxysome polypeptide
BP: Major carboxysome shell protein 1A
CP: Major carboxysome shell protein 1A
DP: Major carboxysome shell protein 1A
AQ: Unidentified carboxysome polypeptide
BQ: Major carboxysome shell protein 1A
CQ: Major carboxysome shell protein 1A
DQ: Major carboxysome shell protein 1A
AR: Unidentified carboxysome polypeptide
BR: Major carboxysome shell protein 1A
CR: Major carboxysome shell protein 1A
DR: Major carboxysome shell protein 1A
AS: Unidentified carboxysome polypeptide
BS: Major carboxysome shell protein 1A
CS: Major carboxysome shell protein 1A
DS: Major carboxysome shell protein 1A
AT: Unidentified carboxysome polypeptide
BT: Major carboxysome shell protein 1A
CT: Major carboxysome shell protein 1A
DT: Major carboxysome shell protein 1A
AV: Unidentified carboxysome polypeptide
BV: Major carboxysome shell protein 1A
CV: Major carboxysome shell protein 1A
DV: Major carboxysome shell protein 1A
AW: Unidentified carboxysome polypeptide
BW: Major carboxysome shell protein 1A
CW: Major carboxysome shell protein 1A
DW: Major carboxysome shell protein 1A
AX: Unidentified carboxysome polypeptide
BX: Major carboxysome shell protein 1A
CX: Major carboxysome shell protein 1A
DX: Major carboxysome shell protein 1A
AY: Unidentified carboxysome polypeptide
BY: Major carboxysome shell protein 1A
CY: Major carboxysome shell protein 1A
DY: Major carboxysome shell protein 1A
AZ: Unidentified carboxysome polypeptide
BZ: Major carboxysome shell protein 1A
CZ: Major carboxysome shell protein 1A
DZ: Major carboxysome shell protein 1A
Aa: Unidentified carboxysome polypeptide
Ba: Major carboxysome shell protein 1A
Ca: Major carboxysome shell protein 1A
Da: Major carboxysome shell protein 1A
Ab: Unidentified carboxysome polypeptide
Bb: Major carboxysome shell protein 1A
Cb: Major carboxysome shell protein 1A
Db: Major carboxysome shell protein 1A
Ac: Unidentified carboxysome polypeptide
Bc: Major carboxysome shell protein 1A
Cc: Major carboxysome shell protein 1A
Dc: Major carboxysome shell protein 1A
Ad: Unidentified carboxysome polypeptide
Bd: Major carboxysome shell protein 1A
Cd: Major carboxysome shell protein 1A
Dd: Major carboxysome shell protein 1A
Ae: Unidentified carboxysome polypeptide
Be: Major carboxysome shell protein 1A
Ce: Major carboxysome shell protein 1A
De: Major carboxysome shell protein 1A
Af: Unidentified carboxysome polypeptide
Bf: Major carboxysome shell protein 1A
Cf: Major carboxysome shell protein 1A
Df: Major carboxysome shell protein 1A
Ag: Unidentified carboxysome polypeptide
Bg: Major carboxysome shell protein 1A
Cg: Major carboxysome shell protein 1A
Dg: Major carboxysome shell protein 1A
Ah: Unidentified carboxysome polypeptide
Bh: Major carboxysome shell protein 1A
Ch: Major carboxysome shell protein 1A
Dh: Major carboxysome shell protein 1A
Ai: Unidentified carboxysome polypeptide
Bi: Major carboxysome shell protein 1A
Ci: Major carboxysome shell protein 1A
Di: Major carboxysome shell protein 1A
Aj: Unidentified carboxysome polypeptide
Bj: Major carboxysome shell protein 1A
Cj: Major carboxysome shell protein 1A
Dj: Major carboxysome shell protein 1A
Ak: Unidentified carboxysome polypeptide
Bk: Major carboxysome shell protein 1A
Ck: Major carboxysome shell protein 1A
Dk: Major carboxysome shell protein 1A
Al: Unidentified carboxysome polypeptide
Bl: Major carboxysome shell protein 1A
Cl: Major carboxysome shell protein 1A
Dl: Major carboxysome shell protein 1A
Am: Unidentified carboxysome polypeptide
Bm: Major carboxysome shell protein 1A
Cm: Major carboxysome shell protein 1A
Dm: Major carboxysome shell protein 1A
An: Unidentified carboxysome polypeptide
Bn: Major carboxysome shell protein 1A
Cn: Major carboxysome shell protein 1A
Dn: Major carboxysome shell protein 1A
Ao: Unidentified carboxysome polypeptide
Bo: Major carboxysome shell protein 1A
Co: Major carboxysome shell protein 1A
Do: Major carboxysome shell protein 1A
Ap: Unidentified carboxysome polypeptide
Bp: Major carboxysome shell protein 1A
Cp: Major carboxysome shell protein 1A
Dp: Major carboxysome shell protein 1A
Aq: Unidentified carboxysome polypeptide
Bq: Major carboxysome shell protein 1A
Cq: Major carboxysome shell protein 1A
Dq: Major carboxysome shell protein 1A
Ar: Unidentified carboxysome polypeptide
Br: Major carboxysome shell protein 1A
Cr: Major carboxysome shell protein 1A
Dr: Major carboxysome shell protein 1A
As: Unidentified carboxysome polypeptide
Bs: Major carboxysome shell protein 1A
Cs: Major carboxysome shell protein 1A
Ds: Major carboxysome shell protein 1A
At: Unidentified carboxysome polypeptide
Bt: Major carboxysome shell protein 1A
Ct: Major carboxysome shell protein 1A
Dt: Major carboxysome shell protein 1A
Av: Unidentified carboxysome polypeptide
Bv: Major carboxysome shell protein 1A
Cv: Major carboxysome shell protein 1A
Dv: Major carboxysome shell protein 1A
Aw: Unidentified carboxysome polypeptide
Bw: Major carboxysome shell protein 1A
Cw: Major carboxysome shell protein 1A
Dw: Major carboxysome shell protein 1A
Ax: Unidentified carboxysome polypeptide
Bx: Major carboxysome shell protein 1A
Cx: Major carboxysome shell protein 1A
Dx: Major carboxysome shell protein 1A
Ay: Unidentified carboxysome polypeptide
By: Major carboxysome shell protein 1A
Cy: Major carboxysome shell protein 1A
Dy: Major carboxysome shell protein 1A
Az: Unidentified carboxysome polypeptide
Bz: Major carboxysome shell protein 1A
Cz: Major carboxysome shell protein 1A
Dz: Major carboxysome shell protein 1A
A0: Unidentified carboxysome polypeptide
B0: Major carboxysome shell protein 1A
C0: Major carboxysome shell protein 1A
D0: Major carboxysome shell protein 1A
A1: Unidentified carboxysome polypeptide
B1: Major carboxysome shell protein 1A
C1: Major carboxysome shell protein 1A
D1: Major carboxysome shell protein 1A
A2: Unidentified carboxysome polypeptide
B2: Major carboxysome shell protein 1A
C2: Major carboxysome shell protein 1A
D2: Major carboxysome shell protein 1A
A3: Unidentified carboxysome polypeptide
B3: Major carboxysome shell protein 1A
C3: Major carboxysome shell protein 1A
D3: Major carboxysome shell protein 1A
A4: Unidentified carboxysome polypeptide
B4: Major carboxysome shell protein 1A
C4: Major carboxysome shell protein 1A
D4: Major carboxysome shell protein 1A
A5: Unidentified carboxysome polypeptide
B5: Major carboxysome shell protein 1A
C5: Major carboxysome shell protein 1A
D5: Major carboxysome shell protein 1A
A6: Unidentified carboxysome polypeptide
B6: Major carboxysome shell protein 1A
C6: Major carboxysome shell protein 1A
D6: Major carboxysome shell protein 1A
A7: Unidentified carboxysome polypeptide
B7: Major carboxysome shell protein 1A
C7: Major carboxysome shell protein 1A
D7: Major carboxysome shell protein 1A
A8: Unidentified carboxysome polypeptide
B8: Major carboxysome shell protein 1A
C8: Major carboxysome shell protein 1A
D8: Major carboxysome shell protein 1A
A9: Unidentified carboxysome polypeptide
B9: Major carboxysome shell protein 1A
C9: Major carboxysome shell protein 1A
D9: Major carboxysome shell protein 1A


Theoretical massNumber of molelcules
Total (without water)2,405,644240
Polymers2,405,644240
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Unidentified carboxysome polypeptide / CsoS4A


Mass: 10173.640 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: O85043
#2: Protein ...
Major carboxysome shell protein 1A / CsoS1A


Mass: 9973.478 Da / Num. of mol.: 180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus (strain ATCC 23641 / c2) (bacteria)
Strain: ATCC 23641 / c2 / Gene: csoS1A, Hneap_0915 / Production host: Escherichia coli (E. coli) / References: UniProt: P45689

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Simplified Alpha-Carboxysome, T=4 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 2.3 MDa / Experimental value: NO
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 64.3 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1RELION3.0.7particle selectionParticles were extracted in RELION
4CTFFIND4.1CTF correctionCTFFIND in RELION was used
7UCSF Chimera1.14model fitting
12RELION3.0.73D reconstructionRELION software was used throughout
13PHENIX1.18.2-3874model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 94129
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67192 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
12RCF

2rcf

12RCF1PDBexperimental model
22EWH

2ewh

12EWH2PDBexperimental model

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