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Yorodumi- EMDB-9296: Cryo-EM structure of the HO BMC shell: Fully asymmetric reconstruction -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9296 | |||||||||
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Title | Cryo-EM structure of the HO BMC shell: Fully asymmetric reconstruction | |||||||||
Map data | Fully asymmetric reconstruction of the HO BMC shell | |||||||||
Sample |
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Function / homology | Function and homology information | |||||||||
Biological species | Haliangium ochraceum (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Greber BJ / Sutter M / Kerfeld CA | |||||||||
Citation | Journal: Structure / Year: 2019 Title: The Plasticity of Molecular Interactions Governs Bacterial Microcompartment Shell Assembly. Authors: Basil J Greber / Markus Sutter / Cheryl A Kerfeld / Abstract: Bacterial microcompartments (BMCs) are composed of an enzymatic core encapsulated by a selectively permeable protein shell that enhances catalytic efficiency. Many pathogenic bacteria derive ...Bacterial microcompartments (BMCs) are composed of an enzymatic core encapsulated by a selectively permeable protein shell that enhances catalytic efficiency. Many pathogenic bacteria derive competitive advantages from their BMC-based catabolism, implicating BMCs as drug targets. BMC shells are of interest for bioengineering due to their diverse and selective permeability properties and because they self-assemble. A complete understanding of shell composition and organization is a prerequisite for biotechnological applications. Here, we report the cryoelectron microscopy structure of a BMC shell at 3.0-Å resolution, using an image-processing strategy that allowed us to determine the previously uncharacterized structural details of the interactions formed by the BMC-T and BMC-T shell subunits in the context of the assembled shell. We found unexpected structural plasticity among these interactions, resulting in distinct shell populations assembled from varying numbers of the BMC-T and BMC-T subunits. We discuss the implications of these findings on shell assembly and function. | |||||||||
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_9296.map.gz | 480.9 MB | EMDB map data format | |
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Header (meta data) | emd-9296-v30.xml emd-9296.xml | 19.6 KB 19.6 KB | Display Display | EMDB header |
Images | emd_9296.png | 203.9 KB | ||
Others | emd_9296_half_map_1.map.gz emd_9296_half_map_2.map.gz | 411.6 MB 410.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9296 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9296 | HTTPS FTP |
-Validation report
Summary document | emd_9296_validation.pdf.gz | 78.7 KB | Display | EMDB validaton report |
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Full document | emd_9296_full_validation.pdf.gz | 77.8 KB | Display | |
Data in XML | emd_9296_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9296 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9296 | HTTPS FTP |
-Related structure data
Related structure data | 9307C 9308C 9309C 9310C 9311C 9312C 9313C 9314C 9315C 6mzuC 6mzvC 6mzxC 6mzyC 6n06C 6n07C 6n09C 6n0fC 6n0gC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9296.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Fully asymmetric reconstruction of the HO BMC shell | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Unfiltered half-map
File | emd_9296_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half-map
File | emd_9296_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Bacterial microcompartment shell from Haliangium ochraceum
Entire | Name: Bacterial microcompartment shell from Haliangium ochraceum |
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Components |
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-Supramolecule #1: Bacterial microcompartment shell from Haliangium ochraceum
Supramolecule | Name: Bacterial microcompartment shell from Haliangium ochraceum type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Haliangium ochraceum (bacteria) |
Molecular weight | Theoretical: 6.5 MDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING Details: Protochips C-flat 1.2/1.3 holey carbon grids were coated with a thin carbon film and plasma cleaned using a Gatan Solarus. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: 5-7 sec incubation of the sample on the grid before blotting and plunging. |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 928 / Average exposure time: 4.5 sec. / Average electron dose: 25.0 e/Å2 Details: 928 images retained after inspection for image quality. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 48543 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |