[English] 日本語
Yorodumi- EMDB-9307: Structure of the HO BMC shell: BMC-TD focused structure, closed state -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9307 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the HO BMC shell: BMC-TD focused structure, closed state | |||||||||
Map data | Asymmetric reconstruction, BMC-T2, closed state | |||||||||
Sample |
| |||||||||
Keywords | microcompartment / shell / compartmentalization / BMC fold / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Haliangium ochraceum (bacteria) / Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Greber BJ / Sutter M / Kerfeld CA | |||||||||
Funding support | United States, 2 items
| |||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9307.map.gz | 12.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-9307-v30.xml emd-9307.xml | 18 KB 18 KB | Display Display | EMDB header |
Images | emd_9307.png | 150.5 KB | ||
Filedesc metadata | emd-9307.cif.gz | 6.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9307 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9307 | 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 (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_9307.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Asymmetric reconstruction, BMC-T2, closed state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Bacterial microcompartment shell from Haliangium ochraceum
Entire | Name: Bacterial microcompartment shell from Haliangium ochraceum |
---|---|
Components |
|
-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 |
---|---|
Source (natural) | Organism: Haliangium ochraceum (bacteria) |
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 |
---|---|
Source (natural) | Organism: Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria) Strain: DSM 14365 / JCM 11303 / SMP-2 |
Molecular weight | Theoretical: 22.904137 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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 |
---|---|
Source (natural) | Organism: Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria) Strain: DSM 14365 / JCM 11303 / SMP-2 |
Molecular weight | Theoretical: 10.126718 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MADALGMIEV RGFVGMVEAA DAMVKAAKVE LIGYEKTGGG YVTAVVRGDV AAVKAATEAG QRAAERVGEV VAVHVIPRPH VNVDAALPL GRTPGMDKSA UniProtKB: Bacterial microcompartment protein homohexamer |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.4 Component:
| ||||||||||||
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. |
-Electron microscopy
Microscope | FEI TITAN |
---|---|
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 FIELDBright-field microscopy / Cs: 2.7 mm |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
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. |
-Image processing
Particle selection | Number selected: 31800 Details: 1000 particles were picked manually to generate reference templates for subsequent auto-picking in RELION 1.4. |
---|---|
Startup model | Type of model: EMDB MAP EMDB ID: Details: The reference was re-scaled and placed in a 512x512x512 pixel box to match the pixel size and appropriate box size for the data. |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.4) |
Final 3D classification | Number classes: 2 / Avg.num./class: 140850 / Software - Name: RELION (ver. 1.4) Details: Focused 3D classification after symmetry expansion of the particle dataset. |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.4) |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) Details: The selected particle subset was refined without masking and subsequently masked to reveal only the subregion of the BMC shell to which the focused classification had been applied. Number images used: 132076 |