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Yorodumi- PDB-9fch: P116 dimer in the full state (PDB structure of the full-length ec... -
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-Basic information
Entry | Database: PDB / ID: 9fch | ||||||
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Title | P116 dimer in the full state (PDB structure of the full-length ectodomain truncated to amino acids 246-818) | ||||||
Components | Uncharacterized protein MG075 homolog | ||||||
Keywords | LIPID BINDING PROTEIN / Lipid Transfer Protein / Mycoplasma pneumoniae | ||||||
Function / homology | membrane / Uncharacterized protein MG075 homolog Function and homology information | ||||||
Biological species | Mycoplasmoides pneumoniae M129 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.52 Å | ||||||
Authors | Mager, S. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: P116 from Mycoplasma is a self-sufficient lipid uptake and delivery machinery Authors: Manger, S. #1: 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 | 9fch.cif.gz | 226.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9fch.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9fch.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9fch_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 9fch_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 9fch_validation.xml.gz | 41.9 KB | Display | |
Data in CIF | 9fch_validation.cif.gz | 60.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/9fch ftp://data.pdbj.org/pub/pdb/validation_reports/fc/9fch | HTTPS FTP |
-Related structure data
Related structure data | 50314MC 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: 64386.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasmoides pneumoniae M129 (bacteria) Gene: MPN_213, G07_orf1030, MP618 / Production host: Escherichia coli (E. coli) / 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 from Mycoplasma pneumoniae (aa 246-818; full state) Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Mycoplasmoides pneumoniae M129 (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 / Details: 20 mM Tris-HCl |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: C-flat-1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 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 defocus max: 3500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 6.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145945 / Symmetry type: POINT |