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Yorodumi- EMDB-17589: Single particle cryo-EM of the Nap complex of Mycoplasma genitali... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17589 | |||||||||
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Title | Single particle cryo-EM of the Nap complex of Mycoplasma genitalium in the expanded conformation at 7.3 Angstrom resolution. | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Adhesion / Mycoplasma genitalium / CELL ADHESION | |||||||||
Biological species | Mycoplasmoides genitalium G37 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.3 Å | |||||||||
Authors | Sprankel L / Scheffer MP / Frangakis AS | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: PLoS Pathog / Year: 2023 Title: Cryo-electron tomography reveals the binding and release states of the major adhesion complex from Mycoplasma genitalium. Authors: Lasse Sprankel / Margot P Scheffer / Sina Manger / Utz H Ermel / Achilleas S Frangakis / Abstract: The nap particle is an immunogenic surface adhesion complex from Mycoplasma genitalium. It is essential for motility and responsible for binding sialylated oligosaccharides on the surface of the host ...The nap particle is an immunogenic surface adhesion complex from Mycoplasma genitalium. It is essential for motility and responsible for binding sialylated oligosaccharides on the surface of the host cell. The nap particle is composed of two P140-P110 heterodimers, the structure of which was recently solved. However, the interpretation of the mechanism by which the mycoplasma cells orchestrate adhesion remained challenging. Here, we provide cryo-electron tomography structures at ~11 Å resolution, which allow for the distinction between the bound and released state of the nap particle, displaying the in vivo conformational states. Fitting of the atomically resolved structures reveals that bound sialylated oligosaccharides are stabilized by both P110 and P140. Movement of the stalk domains allows for the transfer of conformational changes from the interior of the cell to the binding pocket, thus having the capability of an active release process. It is likely that the same mechanism can be transferred to other Mycoplasma species that belong to the pneumoniae cluster. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17589.map.gz | 96.7 MB | EMDB map data format | |
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Header (meta data) | emd-17589-v30.xml emd-17589.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17589_fsc.xml | 10 KB | Display | FSC data file |
Images | emd_17589.png | 119.4 KB | ||
Masks | emd_17589_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-17589.cif.gz | 4.2 KB | ||
Others | emd_17589_half_map_1.map.gz emd_17589_half_map_2.map.gz | 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17589 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17589 | HTTPS FTP |
-Validation report
Summary document | emd_17589_validation.pdf.gz | 872.3 KB | Display | EMDB validaton report |
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Full document | emd_17589_full_validation.pdf.gz | 871.8 KB | Display | |
Data in XML | emd_17589_validation.xml.gz | 18 KB | Display | |
Data in CIF | emd_17589_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17589 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17589 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17589.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17589_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17589_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17589_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Nap adhesion complex in the expanded conformation
Entire | Name: Nap adhesion complex in the expanded conformation |
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Components |
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-Supramolecule #1: Nap adhesion complex in the expanded conformation
Supramolecule | Name: Nap adhesion complex in the expanded conformation / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Mycoplasmoides genitalium G37 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.025 mg/mL | ||||||||||
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Buffer | pH: 7.4 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum SE / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |