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Yorodumi- EMDB-12253: D3 fusion of pT=4 quasi-symmetric bacterial microcompartment particles -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12253 | |||||||||
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Title | D3 fusion of pT=4 quasi-symmetric bacterial microcompartment particles | |||||||||
Map data | D3 fusion of pT=4 bacterial microcompartment particles | |||||||||
Sample |
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Biological species | Klebsiella pneumoniae (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 22.0 Å | |||||||||
Authors | Kalnins G / Cesle EE | |||||||||
Funding support | Latvia, Czech Republic, 2 items
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Citation | Journal: Protein Sci / Year: 2021 Title: Variety of size and form of GRM2 bacterial microcompartment particles. Authors: Eva Emilija Cesle / Anatolij Filimonenko / Kaspars Tars / Gints Kalnins / Abstract: Bacterial microcompartments (BMCs) are bacterial organelles involved in enzymatic processes, such as carbon fixation, choline, ethanolamine and propanediol degradation, and others. Formed of a semi- ...Bacterial microcompartments (BMCs) are bacterial organelles involved in enzymatic processes, such as carbon fixation, choline, ethanolamine and propanediol degradation, and others. Formed of a semi-permeable protein shell and an enzymatic core, they can enhance enzyme performance and protect the cell from harmful intermediates. With the ability to encapsulate non-native enzymes, BMCs show high potential for applied use. For this goal, a detailed look into shell form variability is significant to predict shell adaptability. Here we present four novel 3D cryo-EM maps of recombinant Klebsiella pneumoniae GRM2 BMC shell particles with the resolution in range of 9 to 22 Å and nine novel 2D classes corresponding to discrete BMC shell forms. These structures reveal icosahedral, elongated, oblate, multi-layered and polyhedral traits of BMCs, indicating considerable variation in size and form as well as adaptability during shell formation processes. | |||||||||
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_12253.map.gz | 81 MB | EMDB map data format | |
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Header (meta data) | emd-12253-v30.xml emd-12253.xml | 18.3 KB 18.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12253_fsc.xml | 13.9 KB | Display | FSC data file |
Images | emd_12253.png | 59.8 KB | ||
Others | emd_12253_half_map_1.map.gz emd_12253_half_map_2.map.gz | 80.9 MB 80.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12253 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12253 | HTTPS FTP |
-Validation report
Summary document | emd_12253_validation.pdf.gz | 395.3 KB | Display | EMDB validaton report |
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Full document | emd_12253_full_validation.pdf.gz | 394.4 KB | Display | |
Data in XML | emd_12253_validation.xml.gz | 16.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12253 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12253 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_12253.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | D3 fusion of pT=4 bacterial microcompartment particles | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.44 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_12253_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12253_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : D3 fusion of pT=4 quasi-symmetric bacterial microcompartment particles
Entire | Name: D3 fusion of pT=4 quasi-symmetric bacterial microcompartment particles |
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Components |
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-Supramolecule #1: D3 fusion of pT=4 quasi-symmetric bacterial microcompartment particles
Supramolecule | Name: D3 fusion of pT=4 quasi-symmetric bacterial microcompartment particles type: complex / ID: 1 / Parent: 0 / Macromolecule list: all 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) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Macromolecule #1: cmcC/PduA/ccmK BMC-H bacterial microcompartment protein
Macromolecule | Name: cmcC/PduA/ccmK BMC-H 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: MKEALGLIET KGLVACIEAA DAMCKAANVE LIGYENVGSG LVTAMVKGDV GAVNAAVDSG VEAAKRIGKV VSSRVIARPH NDIEKIAGST KHKSLRPHNA |
-Macromolecule #2: cmcD/EutN BMC-P bacterial microcompartment protein
Macromolecule | Name: cmcD/EutN BMC-P 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: MILAKVTGHV VATQKCDELR GSNLLLITRL DDKQQPMKDQ TWVAVDNVGA GMHDIVLAEE YFALNKDRYK AMSVVAIVEK VFRDTEQE |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 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 / Support film - topology: HOLEY | ||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4s before plunging. | ||||||
Details | Sample was purified with ultracentrifugation and 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: 3240 / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.7000000000000001 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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 |