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- EMDB-18629: Sub-tomogram average of P116 from Mycoplasma pneumoniae tethered ... -

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Basic information

Entry
Database: EMDB / ID: EMD-18629
TitleSub-tomogram average of P116 from Mycoplasma pneumoniae tethered to the mycoplasma membrane (front views only).
Map dataSub-tomogram average of P116 from Mycoplasma pneumoniae tethered to the mycoplasma membrane (front views only).
Sample
  • Complex: Sub-tomogram average of P116 from Mycoplasma pneumoniae tethered to the mycoplasma membrane (front views only).
KeywordsLipid Shuttle Mycoplasma pneumoniae / LIPID BINDING PROTEIN
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
Methodelectron tomography / cryo EM
AuthorsManger S
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) 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
DepositionOct 10, 2023-
Header (metadata) releaseNov 29, 2023-
Map releaseNov 29, 2023-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18629.png

Downloads & links

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Map

FileDownload / File: emd_18629.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSub-tomogram average of P116 from Mycoplasma pneumoniae tethered to the mycoplasma membrane (front views only).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.44 Å/pix.
x 128 pix.
= 568.32 Å		4.44 Å/pix.
x 128 pix.
= 568.32 Å		4.44 Å/pix.
x 128 pix.
= 568.32 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.44 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-4.4226503 - 8.781199000000001
Average (Standard dev.)-0.000000000013737 (±0.99999976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 568.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Sub-tomogram average of P116 from Mycoplasma pneumoniae tethered ...

EntireName: Sub-tomogram average of P116 from Mycoplasma pneumoniae tethered to the mycoplasma membrane (front views only).
Components
  • Complex: Sub-tomogram average of P116 from Mycoplasma pneumoniae tethered to the mycoplasma membrane (front views only).

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Supramolecule #1: Sub-tomogram average of P116 from Mycoplasma pneumoniae tethered ...

SupramoleculeName: Sub-tomogram average of P116 from Mycoplasma pneumoniae tethered to the mycoplasma membrane (front views only).
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: PBS
GridModel: C-flat-1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV
Details: A 3.5 uL drop was applied to a (45 s) glow-discharged R1.2/1.3 C-flat grid (Electron Microscopy Science) with a 4 nm carbon-coat, and plunge-frozen in liquid ethane at 100 percent relative ...Details: A 3.5 uL drop was applied to a (45 s) glow-discharged R1.2/1.3 C-flat grid (Electron Microscopy Science) with a 4 nm carbon-coat, and plunge-frozen in liquid ethane at 100 percent relative humidity, 4degC, and a nominal blot force of -1, with a wait and blotting time of 8-12 s..
DetailsTomography on intact M. pneumoniae cells.
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DetailsTilt-series were recorded using SerialEM v4.0.1423 at a nominal magnification of 81,000 (1.112 A per pixel) in nanoprobe EFTEM mode at 300 kV with a Titan Krios G2 (Thermo Fischer Scientific) electron microscope equipped with a BioQuantum-K3 imaging filter (Gatan), operated in zero-loss peak mode with 20 eV energy slit width, and a K3 Summit detector (Gatan). The total dose per tomogram was 120 e-/A2, and the tilt series covered an angular range from -60deg to 60deg with an angular increment of 3deg and a defocus set at -3 um.
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.0 e/Å2
Details: The total dose per tomogram was 120 e-/A2, and the tilt series covered an angular range from -60deg to 60deg with an angular increment of 3deg
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: RELION (ver. 3,1)
Details: Resolution approx. 30A. Only front views were used (and only the front view of the sub-tomogram average was analyzed.
Number images used: 41

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