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- EMDB-9307: Structure of the HO BMC shell: BMC-TD focused structure, closed state -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9307 | |||||||||
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Title | Structure of the HO BMC shell: BMC-TD focused structure, closed state | |||||||||
![]() | Asymmetric reconstruction, BMC-T2, closed state | |||||||||
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![]() | microcompartment / shell / compartmentalization / BMC fold / STRUCTURAL PROTEIN | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Greber BJ / Sutter M / Kerfeld CA | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 12.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18 KB 18 KB | Display Display | ![]() |
Images | ![]() | 150.5 KB | ||
Filedesc metadata | ![]() | 6.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6mzuMC ![]() 9296C ![]() 9308C ![]() 9309C ![]() 9310C ![]() 9311C ![]() 9312C ![]() 9313C ![]() 9314C ![]() 9315C ![]() 6mzvC ![]() 6mzxC ![]() 6mzyC ![]() 6n06C ![]() 6n07C ![]() 6n09C ![]() 6n0fC ![]() 6n0gC 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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Asymmetric reconstruction, BMC-T2, closed state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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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: ![]() |
Molecular weight | Theoretical: 6.5 MDa |
-Macromolecule #1: Microcompartments protein
Macromolecule | Name: Microcompartments protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: DSM 14365 / JCM 11303 / SMP-2 |
Molecular weight | Theoretical: 22.904137 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSITLRTYIF LDALQPQLAT FIGKTARGFL PVPGQASLWV EIAPGIAINR VTDAALKATK VQPAVQVVER AYGLLEVHHF DQGEVLAAG STILDKLEVR EEGRLKPQVM THQIIRAVEA YQTQIINRNS QGMMILPGES LFILETQPAG YAVLAANEAE K AANVHLVN ...String: MSITLRTYIF LDALQPQLAT FIGKTARGFL PVPGQASLWV EIAPGIAINR VTDAALKATK VQPAVQVVER AYGLLEVHHF DQGEVLAAG STILDKLEVR EEGRLKPQVM THQIIRAVEA YQTQIINRNS QGMMILPGES LFILETQPAG YAVLAANEAE K AANVHLVN VTPYGAFGRL YLAGSEAEID AAAEAAEAAI RSVSGVAQES FRDR UniProtKB: Bacterial microcompartment protein trimer-2 |
-Macromolecule #2: Microcompartments protein
Macromolecule | Name: Microcompartments protein / type: protein_or_peptide / ID: 2 / Number of copies: 36 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: DSM 14365 / JCM 11303 / SMP-2 |
Molecular weight | Theoretical: 10.126718 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MADALGMIEV RGFVGMVEAA DAMVKAAKVE LIGYEKTGGG YVTAVVRGDV AAVKAATEAG QRAAERVGEV VAVHVIPRPH VNVDAALPL GRTPGMDKSA UniProtKB: Bacterial microcompartment protein homohexamer |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | 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 / Details: unspecified | ||||||||||||
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. |
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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 - 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: ![]() |
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 |