[English] 日本語
Yorodumi- EMDB-15275: Single Particle cryo-EM of the empty lipid binding protein P116 (... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15275 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Single Particle cryo-EM of the empty lipid binding protein P116 (MPN213) from Mycoplasma pneumoniae at 4 Angstrom resolution | ||||||||||||
Map data | |||||||||||||
Sample |
| ||||||||||||
Function / homology | membrane / Uncharacterized protein MG075 homolog Function and homology information | ||||||||||||
Biological species | Mycoplasma pneumoniae M129 (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | ||||||||||||
Authors | Sprankel L / Vizarraga D | ||||||||||||
Funding support | Germany, 3 items
| ||||||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_15275.map.gz | 59.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-15275-v30.xml emd-15275.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
Images | emd_15275.png | 33.5 KB | ||
Masks | emd_15275_msk_1.map | 64 MB | Mask map | |
Others | emd_15275_half_map_1.map.gz emd_15275_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15275 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15275 | HTTPS FTP |
-Related structure data
Related structure data | 8a9bMC 8a9aC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_15275.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.662 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_15275_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_15275_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_15275_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Empty P116 monomer
Entire | Name: Empty P116 monomer |
---|---|
Components |
|
-Supramolecule #1: Empty P116 monomer
Supramolecule | Name: Empty P116 monomer / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Mycoplasma pneumoniae M129 (bacteria) |
-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 |
---|---|
Source (natural) | Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 |
Molecular weight | Theoretical: 114.149852 KDa |
Recombinant expression | Organism: Escherichia coli B83 (bacteria) |
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 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
---|---|
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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
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 FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Specialist optics | Energy filter - Name: GIF Quantum SE / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 4532601 |
---|---|
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 633332 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
---|---|
Output model | PDB-8a9b: |