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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4595 | |||||||||
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Title | T=4 quasi-symmetric bacterial microcompartment particle | |||||||||
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Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Kalnins G | |||||||||
![]() | ![]() Title: Encapsulation mechanisms and structural studies of GRM2 bacterial microcompartment particles. Authors: Gints Kalnins / Eva-Emilija Cesle / Juris Jansons / Janis Liepins / Anatolij Filimonenko / Kaspars Tars / ![]() ![]() Abstract: Bacterial microcompartments (BMCs) are prokaryotic organelles consisting of a protein shell and an encapsulated enzymatic core. BMCs are involved in several biochemical processes, such as choline, ...Bacterial microcompartments (BMCs) are prokaryotic organelles consisting of a protein shell and an encapsulated enzymatic core. BMCs are involved in several biochemical processes, such as choline, glycerol and ethanolamine degradation and carbon fixation. Since non-native enzymes can also be encapsulated in BMCs, an improved understanding of BMC shell assembly and encapsulation processes could be useful for synthetic biology applications. Here we report the isolation and recombinant expression of BMC structural genes from the Klebsiella pneumoniae GRM2 locus, the investigation of mechanisms behind encapsulation of the core enzymes, and the characterization of shell particles by cryo-EM. We conclude that the enzymatic core is encapsulated in a hierarchical manner and that the CutC choline lyase may play a secondary role as an adaptor protein. We also present a cryo-EM structure of a pT = 4 quasi-symmetric icosahedral shell particle at 3.3 Å resolution, and demonstrate variability among the minor shell forms. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 115.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.3 KB 19.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.2 KB | Display | ![]() |
Images | ![]() | 115.5 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() | 95.7 MB 95.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qn1MC ![]() 4596C ![]() 4597C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_4595_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_4595_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : T=4 quasi-symmetric bacterial microcompartment particle
Entire | Name: T=4 quasi-symmetric bacterial microcompartment particle |
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Components |
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-Supramolecule #1: T=4 quasi-symmetric bacterial microcompartment particle
Supramolecule | Name: T=4 quasi-symmetric bacterial microcompartment particle type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Bacterial microcompartment particle made by coexpression of shell proteins |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 2.45 MDa |
-Macromolecule #1: Carbon dioxide concentrating mechanism protein CcmL
Macromolecule | Name: Carbon dioxide concentrating mechanism protein CcmL / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 9.962463 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MILAKVTGHV VATQKCDELR GSNLLLITRL DDKQQPMKDQ TWVAVDNVGA GMHDIVLAEE YFALNKDRYK AMSVVAIVEK VFRDTEQE UniProtKB: Carbon dioxide concentrating mechanism protein CcmL |
-Macromolecule #2: BMC domain-containing protein
Macromolecule | Name: BMC domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 180 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 10.309946 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MKEALGLIET KGLVACIEAA DAMCKAANVE LIGYENVGSG LVTAMVKGDV GAVNAAVDSG VEAAKRIGKV VSSRVIARPH NDIEKIAGS TKHKSLRPHN A UniProtKB: BMC domain-containing protein |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON | |||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4 seconds before plunging. | |||||||||
Details | Sample was purified with gel filtration |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD![]() |
Specialist optics | Phase plate: VOLTA PHASE PLATE |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 1316 / Average exposure time: 1.0 sec. / Average electron dose: 60.0 e/Å2 |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 149.892 | ||||||
Output model | ![]() PDB-6qn1: |