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Yorodumi- EMDB-15276: Single Particle cryo-EM of the lipid binding protein P116 (MPN213... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15276 | ||||||||||||
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Title | Single Particle cryo-EM of the lipid binding protein P116 (MPN213) refilled with FBS from Mycoplasma pneumoniae at 3.5 Angstrom resolution. | ||||||||||||
Map data | |||||||||||||
Sample |
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Biological species | Mycoplasma pneumoniae M129 (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
Authors | Sprankel L / Vizarraga D | ||||||||||||
Funding support | Germany, 3 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15276.map.gz | 484 MB | EMDB map data format | |
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Header (meta data) | emd-15276-v30.xml emd-15276.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15276_fsc.xml | 16.9 KB | Display | FSC data file |
Images | emd_15276.png | 36.4 KB | ||
Masks | emd_15276_msk_1.map | 512 MB | Mask map | |
Others | emd_15276_half_map_1.map.gz emd_15276_half_map_2.map.gz | 475.5 MB 475.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15276 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15276 | HTTPS FTP |
-Validation report
Summary document | emd_15276_validation.pdf.gz | 649.2 KB | Display | EMDB validaton report |
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Full document | emd_15276_full_validation.pdf.gz | 648.8 KB | Display | |
Data in XML | emd_15276_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | emd_15276_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15276 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15276 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15276.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15276_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15276_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15276_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : P116 homodimer refilled
Entire | Name: P116 homodimer refilled |
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Components |
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-Supramolecule #1: P116 homodimer refilled
Supramolecule | Name: P116 homodimer refilled / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mycoplasma pneumoniae M129 (bacteria) |
-Macromolecule #1: P116 refilled with FBS
Macromolecule | Name: P116 refilled with FBS / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycoplasma pneumoniae M129 (bacteria) |
Recombinant expression | Organism: Escherichia coli B83 (bacteria) |
Sequence | String: NKTHQVEHES EQSDFQDIRF GLNSVKLPKA Q PAAATRIT VENGTDKLVN YKSSPQQLFL AKNALKDKLQ GEFDKFLSDA KAFPALTADL QE WVDQQLF NPNQSFFDLS APRSNFTLSS DKKASLDFIF RFTNFTESVQ LLKLPEGVSV VVD SKQSFD YYVNASAQKL ...String: NKTHQVEHES EQSDFQDIRF GLNSVKLPKA Q PAAATRIT VENGTDKLVN YKSSPQQLFL AKNALKDKLQ GEFDKFLSDA KAFPALTADL QE WVDQQLF NPNQSFFDLS APRSNFTLSS DKKASLDFIF RFTNFTESVQ LLKLPEGVSV VVD SKQSFD YYVNASAQKL LVLPLSLPDY TLGLNYMFDH ITLNGKVVNK FSFNPFKTNL NLAF SNVYN GVDVFEAQKN LVGKGKYLNT HVKAEDVKKD VNANIKNQFD IAKIIAELMG KALKE FGNQ QEGQPLSFLK VMDKVKEDFE KLFNLVRPGL GKFVKDLIQS SSQAENKITV YKLIFD NKK TILNLLKELS IPELNSSLGL VDVLFDGITD SDGLYERLQS FKDLIVPAVK TNEKTAA LS PLIEELLTQK DTYVFDLIQK HKGILTNLLK NFLADFQKST PFMADQVAIF TELFDNEG A FDLFGEADFV DKIAELFLTK RTVKNGEKIE TKDSLLVTSL KSLLGEKVAA LGDLLDSYI FKNELLNRSV EVAKAEAKDT KGATDYKKEQ AKALKKLFKH IGENTLSKTN LDKITLKEVK NTENVELEE TETTLKVKKL DVEYKVELGN FEIKNGLIKA MLEFLPDTKD LETTLDKLLF K GESYKAMK DKYIKEGFPG YGWAKGVVPG AFESIENTFK SAIDKTKSIR DLFGDMLFGN DL SSVKETD SFITLGGSFD IKYGGENLNV LPAYYSLINS EIGYQIIGVD TTIDATKVKV ELK NKEYKG KSPAINGQVK LSQSFFNVWT NMFDSITKQI FQKKYEFKDN IQVFARNEDN TSRL ELDIS DPEQRVIPFA FVDGFGIQLK AVDKNITKEA GNTEPKSPVI QLYEALNKEK DQKQQ SKQS PKQLDTKTQL GYLLKLGDNW SKDDYKSLID DTIINNNYLE ASFNSKITVD RLGIPI DLW LFKIWPKFNL EIPMQGSLQL YSSSVIFPYG IYDTSVQDAA KIVKRLNFTD MGFKLND PK PNFWFVGFKH HHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL | ||||||
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Buffer | pH: 7.4 / Component:
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-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 K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Number grids imaged: 1 / Number real images: 4019 / Average electron dose: 50.0 e/Å2 |
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 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 |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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