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Yorodumi- PDB-8a9a: Single Particle cryo-EM of the lipid binding protein P116 (MPN213... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a9a | ||||||||||||
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Title | Single Particle cryo-EM of the lipid binding protein P116 (MPN213) from Mycoplasma pneumoniae at 3.3 Angstrom resolution. | ||||||||||||
Components | Lipid binding protein P116 (MPN213) | ||||||||||||
Keywords | LIPID BINDING PROTEIN / Lipid binding protein P116 (MPN213) from Mycoplasma pneumoniae / LIPID BINDING | ||||||||||||
Function / homology | membrane / Uncharacterized protein MG075 homolog Function and homology information | ||||||||||||
Biological species | Mycoplasma pneumoniae M129 (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
Authors | Sprankel, L. / Vizarraga, D. | ||||||||||||
Funding support | Germany, 3items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Essential protein P116 extracts cholesterol and other indispensable lipids for Mycoplasmas. Authors: Lasse Sprankel / David Vizarraga / Jesús Martín / Sina Manger / Jakob Meier-Credo / Marina Marcos / Josep Julve / Noemi Rotllan / Margot P Scheffer / Joan Carles Escolà-Gil / Julian D ...Authors: Lasse Sprankel / David Vizarraga / Jesús Martín / Sina Manger / Jakob Meier-Credo / Marina Marcos / Josep Julve / Noemi Rotllan / Margot P Scheffer / Joan Carles Escolà-Gil / Julian D Langer / Jaume Piñol / Ignacio Fita / Achilleas S Frangakis / Abstract: Mycoplasma pneumoniae, responsible for approximately 30% of community-acquired human pneumonia, needs to extract lipids from the host environment for survival and proliferation. Here, we report a ...Mycoplasma pneumoniae, responsible for approximately 30% of community-acquired human pneumonia, needs to extract lipids from the host environment for survival and proliferation. Here, we report a comprehensive structural and functional analysis of the previously uncharacterized protein P116 (MPN_213). Single-particle cryo-electron microscopy of P116 reveals a homodimer presenting a previously unseen fold, forming a huge hydrophobic cavity, which is fully accessible to solvent. Lipidomics analysis shows that P116 specifically extracts lipids such as phosphatidylcholine, sphingomyelin and cholesterol. Structures of different conformational states reveal the mechanism by which lipids are extracted. This finding immediately suggests a way to control Mycoplasma infection by interfering with lipid uptake. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a9a.cif.gz | 330.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a9a.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8a9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a9a_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8a9a_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8a9a_validation.xml.gz | 67.2 KB | Display | |
Data in CIF | 8a9a_validation.cif.gz | 99.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/8a9a ftp://data.pdbj.org/pub/pdb/validation_reports/a9/8a9a | HTTPS FTP |
-Related structure data
Related structure data | 15274MC 8a9bC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 114149.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / Gene: MPN_213, G07_orf1030, MP618 / Production host: Escherichia coli B83 (bacteria) / References: UniProt: P75556 |
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-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 | Name: P116 homodimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||
Source (natural) | Organism: Mycoplasma pneumoniae M129 (bacteria) | ||||||||||||
Source (recombinant) | Organism: Escherichia coli B83 (bacteria) | ||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||
Buffer component |
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Specimen | Conc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 | ||||||||||||
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: 3500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3500 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) / Num. of grids imaged: 1 / Num. of real images: 4376 |
EM imaging optics | Energyfilter name: GIF Quantum SE / Energyfilter slit width: 20 eV |
Image scans | Width: 3710 / Height: 3838 / Movie frames/image: 34 |
-Processing
Software | Name: PHENIX / Version: 1.20_4459: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3463490 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1324330 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
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