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Yorodumi- PDB-8pby: Single particle cryo-EM of the P140-P110 heterodimer with an alte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pby | |||||||||
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Title | Single particle cryo-EM of the P140-P110 heterodimer with an alternative conformation in the P140 stalk of Mycoplasma genitalium at a resolution of 3.7 Angstrom. | |||||||||
Components |
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Keywords | CELL ADHESION / Adhesion / Mycoplasma genitalium | |||||||||
Function / homology | Function and homology information adhesion of symbiont to microvasculature / cell adhesion / plasma membrane Similarity search - Function | |||||||||
Biological species | Mycoplasmoides genitalium G37 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Sprankel, L. / Scheffer, M.P. / Frangakis, A.S. | |||||||||
Funding support | Germany, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pby.cif.gz | 855.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pby.ent.gz | 664.1 KB | Display | PDB format |
PDBx/mmJSON format | 8pby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pby_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8pby_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8pby_validation.xml.gz | 76.8 KB | Display | |
Data in CIF | 8pby_validation.cif.gz | 111.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/8pby ftp://data.pdbj.org/pub/pdb/validation_reports/pb/8pby | HTTPS FTP |
-Related structure data
Related structure data | 17588MC 8pbxC 8pbzC 8pc0C 8pc1C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 115382.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasmoides genitalium G37 (bacteria) Gene: MG192 / Production host: Mycoplasmoides genitalium G37 (bacteria) / References: UniProt: P22747 |
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#2: Protein | Mass: 159809.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides genitalium G37 (bacteria) / References: UniProt: P20796 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Mycoplasmoides genitalium G37 (bacteria) | |||||||||||||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.025 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Calibrated magnification: 130000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 4000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Quantum SE / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67091 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 137.25 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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