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- EMDB-15275: Single Particle cryo-EM of the empty lipid binding protein P116 (... -
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Open data
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Basic information
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Title | Single Particle cryo-EM of the empty lipid binding protein P116 (MPN213) from Mycoplasma pneumoniae at 4 Angstrom resolution | ||||||||||||
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![]() | Empty lipid binding protein P116 (MPN213) from Mycoplasma pneumoniae / LIPID BINDING / LIPID BINDING PROTEIN | ||||||||||||
Function / homology | membrane / Uncharacterized protein MG075 homolog![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | ||||||||||||
![]() | Sprankel L / Vizarraga D | ||||||||||||
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 | ![]() | 59.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.4 KB 17.4 KB | Display Display | ![]() |
Images | ![]() | 33.5 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 59.4 MB 59.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 710.2 KB | Display | ![]() |
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Full document | ![]() | 709.8 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8a9bMC ![]() 8a9aC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.662 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: #1
File | emd_15275_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15275_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Empty P116 monomer
Entire | Name: Empty P116 monomer |
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Components |
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-Supramolecule #1: Empty P116 monomer
Supramolecule | Name: Empty P116 monomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Lipid binding protein P116 (MPN213)
Macromolecule | Name: Lipid binding protein P116 (MPN213) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 114.149852 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: NKTHQVEHES EQSDFQDIRF GLNSVKLPKA QPAAATRITV ENGTDKLVNY KSSPQQLFLA KNALKDKLQG EFDKFLSDAK AFPALTADL QEWVDQQLFN PNQSFFDLSA PRSNFTLSSD KKASLDFIFR FTNFTESVQL LKLPEGVSVV VDSKQSFDYY V NASAQKLL ...String: NKTHQVEHES EQSDFQDIRF GLNSVKLPKA QPAAATRITV ENGTDKLVNY KSSPQQLFLA KNALKDKLQG EFDKFLSDAK AFPALTADL QEWVDQQLFN PNQSFFDLSA PRSNFTLSSD KKASLDFIFR FTNFTESVQL LKLPEGVSVV VDSKQSFDYY V NASAQKLL VLPLSLPDYT LGLNYMFDHI TLNGKVVNKF SFNPFKTNLN LAFSNVYNGV DVFEAQKNLV GKGKYLNTHV KA EDVKKDV NANIKNQFDI AKIIAELMGK ALKEFGNQQE GQPLSFLKVM DKVKEDFEKL FNLVRPGLGK FVKDLIQSSS QAE NKITVY KLIFDNKKTI LNLLKELSIP ELNSSLGLVD VLFDGITDSD GLYERLQSFK DLIVPAVKTN EKTAALSPLI EELL TQKDT YVFDLIQKHK GILTNLLKNF LADFQKSTPF MADQVAIFTE LFDNEGAFDL FGEADFVDKI AELFLTKRTV KNGEK IETK DSLLVTSLKS LLGEKVAALG DLLDSYIFKN ELLNRSVEVA KAEAKDTKGA TDYKKEQAKA LKKLFKHIGE NTLSKT NLD KITLKEVKNT ENVELEETET TLKVKKLDVE YKVELGNFEI KNGLIKAMLE FLPDTKDLET TLDKLLFKGE SYKAMKD KY IKEGFPGYGW AKGVVPGAFE SIENTFKSAI DKTKSIRDLF GDMLFGNDLS SVKETDSFIT LGGSFDIKYG GENLNVLP A YYSLINSEIG YQIIGVDTTI DATKVKVELK NKEYKGKSPA INGQVKLSQS FFNVWTNMFD SITKQIFQKK YEFKDNIQV FARNEDNTSR LELDISDPEQ RVIPFAFVDG FGIQLKAVDK NITKEAGNTE PKSPVIQLYE ALNKEKDQKQ QSKQSPKQLD TKTQLGYLL KLGDNWSKDD YKSLIDDTII NNNYLEASFN SKITVDRLGI PIDLWLFKIW PKFNLEIPMQ GSLQLYSSSV I FPYGIYDT SVQDAAKIVK RLNFTDMGFK LNDPKPNFWF VGFKHHHHH UniProtKB: Uncharacterized protein MG075 homolog |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.4 / Component - Concentration: 20.0 mM / Component - Name: Tris |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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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 K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 15299 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.5 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: 3.5 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 |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-8a9b: |