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- EMDB-18478: P116 (ectodomain AA 246-818) from Mycoplasma pneumoniae empty monomer -
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Open data
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Basic information
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Title | P116 (ectodomain AA 246-818) from Mycoplasma pneumoniae empty monomer | |||||||||
![]() | P116 (ectodomain AA 246-818) from Mycoplasma pneumoniae empty monomer | |||||||||
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![]() | Lipid Shuttle Mycoplasma pneumoniae / LIPID BINDING PROTEIN | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.43 Å | |||||||||
![]() | Manger S | |||||||||
Funding support | ![]()
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![]() | ![]() 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 30.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15 KB 15 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.5 KB | Display | ![]() |
Images | ![]() | 42.7 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Others | ![]() ![]() | 59.4 MB 59.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 635.7 KB | Display | ![]() |
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Full document | ![]() | 635.2 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | P116 (ectodomain AA 246-818) from Mycoplasma pneumoniae empty monomer | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: P116 (ectodomain AA 246-818) from Mycoplasma pneumoniae empty monomer
File | emd_18478_half_map_1.map | ||||||||||||
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Annotation | P116 (ectodomain AA 246-818) from Mycoplasma pneumoniae empty monomer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: P116 (ectodomain AA 246-818) from Mycoplasma pneumoniae empty monomer
File | emd_18478_half_map_2.map | ||||||||||||
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Annotation | P116 (ectodomain AA 246-818) from Mycoplasma pneumoniae empty monomer | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : P116 (ectodomain AA 246-818) from Mycoplasma pneumoniae empty monomer
Entire | Name: P116 (ectodomain AA 246-818) from Mycoplasma pneumoniae empty monomer |
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Components |
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-Supramolecule #1: P116 (ectodomain AA 246-818) from Mycoplasma pneumoniae empty monomer
Supramolecule | Name: P116 (ectodomain AA 246-818) from Mycoplasma pneumoniae empty monomer type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 7.4 / Details: 20 mM Tris-HCl, pH 7.4 0.5 mM CHAPSO |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 8002 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |