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- EMDB-15275: Single Particle cryo-EM of the empty lipid binding protein P116 (... -

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Basic information

Entry
Database: EMDB / ID: EMD-15275
TitleSingle Particle cryo-EM of the empty lipid binding protein P116 (MPN213) from Mycoplasma pneumoniae at 4 Angstrom resolution
Map data
Sample
  • Complex: Empty P116 monomer
    • Protein or peptide: Lipid binding protein P116 (MPN213)
KeywordsEmpty lipid binding protein P116 (MPN213) from Mycoplasma pneumoniae / LIPID BINDING / LIPID BINDING PROTEIN
Function / homology: / : / P116-like protein / membrane / Uncharacterized protein MG075 homolog
Function and homology information
Biological speciesMycoplasma pneumoniae M129 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsSprankel L / Vizarraga D
Funding support Germany, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)FR 1653/14-1 Germany
German Research Foundation (DFG)FR 1653/6-3 Germany
German Research Foundation (DFG)GRK 2566/1 Germany
CitationJournal: 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
DepositionJun 28, 2022-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15275.png

Downloads & links

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Map

FileDownload / File: emd_15275.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 256 pix.
= 425.472 Å		1.66 Å/pix.
x 256 pix.
= 425.472 Å		1.66 Å/pix.
x 256 pix.
= 425.472 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.662 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.34
Minimum - Maximum-6.974575 - 9.906613
Average (Standard dev.)-0.0014526893 (±0.093368046)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 425.472 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15275_msk_1.map
Projections & Slices
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Half map: #1

Fileemd_15275_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_15275_half_map_2.map
Projections & Slices
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Sample components

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Entire : Empty P116 monomer

EntireName: Empty P116 monomer
Components
  • Complex: Empty P116 monomer
    • Protein or peptide: Lipid binding protein P116 (MPN213)

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Supramolecule #1: Empty P116 monomer

SupramoleculeName: Empty P116 monomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria)

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Macromolecule #1: Lipid binding protein P116 (MPN213)

MacromoleculeName: 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 weightTheoretical: 114.149852 KDa
Recombinant expressionOrganism: Escherichia coli B83 (bacteria)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.4 / Component - Concentration: 20.0 mM / Component - Name: Tris
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum SE / Energy filter - Slit width: 20 eV
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen 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

Particle selectionNumber selected: 4532601
CTF correctionSoftware - Name: cryoSPARC (ver. 3.32) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.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
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8a9b:
Single Particle cryo-EM of the empty lipid binding protein P116 (MPN213) from Mycoplasma pneumoniae at 4 Angstrom resolution

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