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- PDB-6owg: Structure of a synthetic beta-carboxysome shell, T=4 -

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Basic information

Entry
Database: PDB / ID: 6owg
TitleStructure of a synthetic beta-carboxysome shell, T=4
Components
  • Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
  • Microcompartments proteinBacterial microcompartment
KeywordsSTRUCTURAL PROTEIN / BACTERIAL MICROCOMPARTMENTS / CARBOXYSOME
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation / photosynthesis
Similarity search - Function
Carboxysome shell vertex protein CcmL / Carboxysome shell protein CcmK / 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 microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain ...Carboxysome shell vertex protein CcmL / Carboxysome shell protein CcmK / 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 microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC
Similarity search - Domain/homology
Carboxysome shell vertex protein CcmL / Carboxysome shell protein CcmK
Similarity search - Component
Biological speciesHalothece sp.
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsSutter, M. / Laughlin, T.G. / Davies, K.M. / Kerfeld, C.A.
CitationJournal: Plant Physiol / Year: 2019
Title: Structure of a Synthetic -Carboxysome Shell.
Authors: Markus Sutter / Thomas G Laughlin / Nancy B Sloan / Daniel Serwas / Karen M Davies / Cheryl A Kerfeld /
Abstract: Carboxysomes are capsid-like, CO-fixing organelles that are present in all cyanobacteria and some chemoautotrophs and that substantially contribute to global primary production. They are composed of ...Carboxysomes are capsid-like, CO-fixing organelles that are present in all cyanobacteria and some chemoautotrophs and that substantially contribute to global primary production. They are composed of a selectively permeable protein shell that encapsulates Rubisco, the principal CO-fixing enzyme, and carbonic anhydrase. As the centerpiece of the carbon-concentrating mechanism, by packaging enzymes that collectively enhance catalysis, the carboxysome shell enables the generation of a locally elevated concentration of substrate CO and the prevention of CO escape. A functional carboxysome consisting of an intact shell and cargo is essential for cyanobacterial growth under ambient CO concentrations. Using cryo-electron microscopy, we have determined the structure of a recombinantly produced simplified β-carboxysome shell. The structure reveals the sidedness and the specific interactions between the carboxysome shell proteins. The model provides insight into the structural basis of selective permeability of the carboxysome shell and can be used to design modifications to investigate the mechanisms of cargo encapsulation and other physiochemical properties such as permeability. Notably, the permeability properties are of great interest for modeling and evaluating this carbon-concentrating mechanism in metabolic engineering. Moreover, we find striking similarity between the carboxysome shell and the structurally characterized, evolutionarily distant metabolosome shell, implying universal architectural principles for bacterial microcompartment shells.
History
DepositionMay 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Dec 18, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Microcompartments protein
B: Microcompartments protein
C: Microcompartments protein
D: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
E: Microcompartments protein
F: Microcompartments protein
G: Microcompartments protein
H: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
I: Microcompartments protein
J: Microcompartments protein
K: Microcompartments protein
L: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
M: Microcompartments protein
N: Microcompartments protein
O: Microcompartments protein
P: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
Q: Microcompartments protein
R: Microcompartments protein
S: Microcompartments protein
T: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
U: Microcompartments protein
V: Microcompartments protein
W: Microcompartments protein
X: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
Y: Microcompartments protein
Z: Microcompartments protein
0: Microcompartments protein
1: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
2: Microcompartments protein
3: Microcompartments protein
4: Microcompartments protein
5: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
6: Microcompartments protein
7: Microcompartments protein
8: Microcompartments protein
9: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
a: Microcompartments protein
b: Microcompartments protein
c: Microcompartments protein
d: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
e: Microcompartments protein
f: Microcompartments protein
g: Microcompartments protein
h: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
i: Microcompartments protein
j: Microcompartments protein
k: Microcompartments protein
l: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
m: Microcompartments protein
n: Microcompartments protein
o: Microcompartments protein
p: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
q: Microcompartments protein
r: Microcompartments protein
s: Microcompartments protein
t: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
u: Microcompartments protein
v: Microcompartments protein
w: Microcompartments protein
x: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
y: Microcompartments protein
z: Microcompartments protein
AA: Microcompartments protein
AB: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AC: Microcompartments protein
AD: Microcompartments protein
AE: Microcompartments protein
AF: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AG: Microcompartments protein
AH: Microcompartments protein
AI: Microcompartments protein
AJ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AK: Microcompartments protein
AL: Microcompartments protein
AM: Microcompartments protein
AN: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AO: Microcompartments protein
AP: Microcompartments protein
AQ: Microcompartments protein
AR: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AS: Microcompartments protein
AT: Microcompartments protein
AU: Microcompartments protein
AV: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AW: Microcompartments protein
AX: Microcompartments protein
AY: Microcompartments protein
AZ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
A0: Microcompartments protein
A1: Microcompartments protein
A2: Microcompartments protein
A3: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
A4: Microcompartments protein
A5: Microcompartments protein
A6: Microcompartments protein
A7: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
A8: Microcompartments protein
A9: Microcompartments protein
BA: Microcompartments protein
BB: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BC: Microcompartments protein
BD: Microcompartments protein
BE: Microcompartments protein
BF: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BG: Microcompartments protein
BH: Microcompartments protein
BI: Microcompartments protein
BJ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BK: Microcompartments protein
BL: Microcompartments protein
BM: Microcompartments protein
BN: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BO: Microcompartments protein
BP: Microcompartments protein
BQ: Microcompartments protein
BR: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BS: Microcompartments protein
BT: Microcompartments protein
BU: Microcompartments protein
BV: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BW: Microcompartments protein
BX: Microcompartments protein
BY: Microcompartments protein
BZ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
B0: Microcompartments protein
B1: Microcompartments protein
B2: Microcompartments protein
B3: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
B4: Microcompartments protein
B5: Microcompartments protein
B6: Microcompartments protein
B7: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
B8: Microcompartments protein
B9: Microcompartments protein
CA: Microcompartments protein
CB: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CC: Microcompartments protein
CD: Microcompartments protein
CE: Microcompartments protein
CF: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CG: Microcompartments protein
CH: Microcompartments protein
CI: Microcompartments protein
CJ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CK: Microcompartments protein
CL: Microcompartments protein
CM: Microcompartments protein
CN: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CO: Microcompartments protein
CP: Microcompartments protein
CQ: Microcompartments protein
CR: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CS: Microcompartments protein
CT: Microcompartments protein
CU: Microcompartments protein
CV: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CW: Microcompartments protein
CX: Microcompartments protein
CY: Microcompartments protein
CZ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
C0: Microcompartments protein
C1: Microcompartments protein
C2: Microcompartments protein
C3: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
C4: Microcompartments protein
C5: Microcompartments protein
C6: Microcompartments protein
C7: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
C8: Microcompartments protein
C9: Microcompartments protein
DA: Microcompartments protein
DB: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
DC: Microcompartments protein
DD: Microcompartments protein
DE: Microcompartments protein
DF: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
DG: Microcompartments protein
DH: Microcompartments protein
DI: Microcompartments protein
DJ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
DK: Microcompartments protein
DL: Microcompartments protein
DM: Microcompartments protein
DN: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
DO: Microcompartments protein
DP: Microcompartments protein
DQ: Microcompartments protein
DR: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
DS: Microcompartments protein
DT: Microcompartments protein
DU: Microcompartments protein
DV: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
DW: Microcompartments protein
DX: Microcompartments protein
DY: Microcompartments protein
DZ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
D0: Microcompartments protein
D1: Microcompartments protein
D2: Microcompartments protein
D3: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
D4: Microcompartments protein
D5: Microcompartments protein
D6: Microcompartments protein
D7: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
D8: Microcompartments protein
D9: Microcompartments protein
EA: Microcompartments protein
EB: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
EC: Microcompartments protein
ED: Microcompartments protein
EE: Microcompartments protein
EF: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
EG: Microcompartments protein
EH: Microcompartments protein
EI: Microcompartments protein
EJ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
EK: Microcompartments protein
EL: Microcompartments protein
EM: Microcompartments protein
EN: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
EO: Microcompartments protein
EP: Microcompartments protein
EQ: Microcompartments protein
ER: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
ES: Microcompartments protein
ET: Microcompartments protein
EU: Microcompartments protein
EV: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
EW: Microcompartments protein
EX: Microcompartments protein
EY: Microcompartments protein
EZ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
E0: Microcompartments protein
E1: Microcompartments protein
E2: Microcompartments protein
E3: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
E4: Microcompartments protein
E5: Microcompartments protein
E6: Microcompartments protein
E7: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml


Theoretical massNumber of molelcules
Total (without water)2,880,053240
Polymers2,880,053240
Non-polymers00
Water0
1


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

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Components

#1: Protein ...
Microcompartments protein / Bacterial microcompartment


Mass: 12163.887 Da / Num. of mol.: 180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothece sp. (strain PCC 7418) (bacteria)
Strain: PCC 7418 / Gene: PCC7418_3532 / Production host: Escherichia coli (E. coli) / References: UniProt: K9YHS7
#2: Protein ...
Ethanolamine utilization protein EutN/carboxysome structural protein Ccml


Mass: 11509.216 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothece sp. (strain PCC 7418) (bacteria)
Strain: PCC 7418 / Gene: PCC7418_3533 / Production host: Escherichia coli (E. coli) / References: UniProt: K9YFK1

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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: Synthetic beta-carboxysome shell (T=4) / Type: COMPLEX / Details: bacterial microcompartment shell / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Halothece sp. PCC 7418 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot for 6 seconds before plunging

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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 / Calibrated magnification: 56000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 2.7 nm / Calibrated defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1343
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 25 eV
Image scansMovie frames/image: 25 / Used frames/image: 1-25

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Processing

EM software
IDNameVersionCategory
1Gautomatch0.56particle selection
2SerialEMimage acquisition
4Gctf1.06CTF correction
5RELION3.0.b2CTF correction
11cryoSPARC2initial Euler assignment
12RELION3.0.b2final Euler assignment
14RELION3.0b23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 47121
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35384 / Symmetry type: POINT

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