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- PDB-6owf: Structure of a synthetic beta-carboxysome shell, T=3 -

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Basic information

Entry
Database: PDB / ID: 6owf
TitleStructure of a synthetic beta-carboxysome shell, T=3
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: 3 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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Assembly

Deposited unit
A: Microcompartments protein
B: Microcompartments protein
C: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
D: Microcompartments protein
E: Microcompartments protein
F: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
G: Microcompartments protein
H: Microcompartments protein
I: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
J: Microcompartments protein
K: Microcompartments protein
L: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
M: Microcompartments protein
N: Microcompartments protein
O: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
P: Microcompartments protein
Q: Microcompartments protein
R: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
S: Microcompartments protein
T: Microcompartments protein
U: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
V: Microcompartments protein
W: Microcompartments protein
X: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
Y: Microcompartments protein
Z: Microcompartments protein
0: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
1: Microcompartments protein
2: Microcompartments protein
3: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
4: Microcompartments protein
5: Microcompartments protein
6: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
7: Microcompartments protein
8: Microcompartments protein
9: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
a: Microcompartments protein
b: Microcompartments protein
c: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
d: Microcompartments protein
e: Microcompartments protein
f: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
g: Microcompartments protein
h: Microcompartments protein
i: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
j: Microcompartments protein
k: Microcompartments protein
l: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
m: Microcompartments protein
n: Microcompartments protein
o: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
p: Microcompartments protein
q: Microcompartments protein
r: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
s: Microcompartments protein
t: Microcompartments protein
u: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
v: Microcompartments protein
w: Microcompartments protein
x: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
y: Microcompartments protein
z: Microcompartments protein
AA: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AB: Microcompartments protein
AC: Microcompartments protein
AD: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AE: Microcompartments protein
AF: Microcompartments protein
AG: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AH: Microcompartments protein
AI: Microcompartments protein
AJ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AK: Microcompartments protein
AL: Microcompartments protein
AM: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AN: Microcompartments protein
AO: Microcompartments protein
AP: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AQ: Microcompartments protein
AR: Microcompartments protein
AS: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AT: Microcompartments protein
AU: Microcompartments protein
AV: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AW: Microcompartments protein
AX: Microcompartments protein
AY: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AZ: Microcompartments protein
A0: Microcompartments protein
A1: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
A2: Microcompartments protein
A3: Microcompartments protein
A4: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
A5: Microcompartments protein
A6: Microcompartments protein
A7: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
A8: Microcompartments protein
A9: Microcompartments protein
BA: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BB: Microcompartments protein
BC: Microcompartments protein
BD: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BE: Microcompartments protein
BF: Microcompartments protein
BG: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BH: Microcompartments protein
BI: Microcompartments protein
BJ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BK: Microcompartments protein
BL: Microcompartments protein
BM: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BN: Microcompartments protein
BO: Microcompartments protein
BP: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BQ: Microcompartments protein
BR: Microcompartments protein
BS: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BT: Microcompartments protein
BU: Microcompartments protein
BV: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BW: Microcompartments protein
BX: Microcompartments protein
BY: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BZ: Microcompartments protein
B0: Microcompartments protein
B1: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
B2: Microcompartments protein
B3: Microcompartments protein
B4: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
B5: Microcompartments protein
B6: Microcompartments protein
B7: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
B8: Microcompartments protein
B9: Microcompartments protein
CA: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CB: Microcompartments protein
CC: Microcompartments protein
CD: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CE: Microcompartments protein
CF: Microcompartments protein
CG: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CH: Microcompartments protein
CI: Microcompartments protein
CJ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CK: Microcompartments protein
CL: Microcompartments protein
CM: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CN: Microcompartments protein
CO: Microcompartments protein
CP: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CQ: Microcompartments protein
CR: Microcompartments protein
CS: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CT: Microcompartments protein
CU: Microcompartments protein
CV: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CW: Microcompartments protein
CX: Microcompartments protein
CY: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CZ: Microcompartments protein
C0: Microcompartments protein
C1: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
C2: Microcompartments protein
C3: Microcompartments protein
C4: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
C5: Microcompartments protein
C6: Microcompartments protein
C7: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
C8: Microcompartments protein
C9: Microcompartments protein
DA: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
DB: Microcompartments protein
DC: Microcompartments protein
DD: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
DE: Microcompartments protein
DF: Microcompartments protein
DG: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
DH: Microcompartments protein
DI: Microcompartments protein
DJ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml


Theoretical massNumber of molelcules
Total (without water)2,150,219180
Polymers2,150,219180
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.: 120
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=3) / 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 min: 500 nm / Calibrated defocus min: 2000 nm / Cs: 2.7 mm
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
13RELION3.0.b2classification
14RELION3.0b23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 47121
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1586 / Symmetry type: POINT

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