+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4596 | |||||||||
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Title | T=4, Q=6 quasi-symmetric bacterial microcompartment particle | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Klebsiella pneumoniae (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.64 Å | |||||||||
Authors | Kalnins G | |||||||||
Citation | Journal: Nat Commun / Year: 2020 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4596.map.gz | 3.1 MB | EMDB map data format | |
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Header (meta data) | emd-4596-v30.xml emd-4596.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4596_fsc.xml | 4.4 KB | Display | FSC data file |
Images | emd_4596.png | 97.2 KB | ||
Others | emd_4596_half_map_1.map.gz emd_4596_half_map_2.map.gz | 3.1 MB 3.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4596 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4596 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4596.map.gz / Format: CCP4 / Size: 4.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 4.7308 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #2
File | emd_4596_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_4596_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : bacterial microcompartment particles
Entire | Name: bacterial microcompartment particles |
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Components |
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-Supramolecule #1: bacterial microcompartment particles
Supramolecule | Name: bacterial microcompartment particles / type: complex / ID: 1 / Parent: 0 Details: bacterial microcompartment particle obtained by recombinant expression of pentameric EutN and hexameric cmcC subunits |
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Source (natural) | Organism: Klebsiella pneumoniae (bacteria) / Strain: MSCL535 |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pET-Duet1 |
Molecular weight | Experimental: 2.55 MDa |
-Macromolecule #1: cmcD/EutN BMC-P bacterial microcompartment protein
Macromolecule | Name: cmcD/EutN BMC-P bacterial microcompartment protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Klebsiella pneumoniae (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MILAKVTGHV VATQKCDELR GSNLLLITRL DDKQQPMKDQ TWVAVDNVGA GMHDIVLAEE YFALNKDRYK AMSVVAIVEK VFRD |
-Macromolecule #2: cmcC/PduA/ccmK BMC-H bacterial microcompartment protein
Macromolecule | Name: cmcC/PduA/ccmK BMC-H bacterial microcompartment protein type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Klebsiella pneumoniae (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MKEALGLIET KGLVACIEAA DAMCKAANVE LIGYENVGSG LVTAMVKGDV GAVNAAVDSG VEAAKRIGEV VSSRVIARPH NDIEKIAG |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 5 seconds before plunging. | |||||||||
Details | Sample was purified with gel filtration |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Specialist optics | Phase plate: VOLTA PHASE PLATE |
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 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: -3.0 µm / Nominal defocus min: -1.4 µm / Nominal magnification: 120000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |