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- EMDB-50307: P116 (aa 246-818) empty dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-50307
TitleP116 (aa 246-818) empty dimer
Map data
Sample
  • Complex: Mycoplasma pneumoniae protein P116 fragment spanning amino acids 246-818 (dimer in empty state)
KeywordsLipid Binding Protein / Lipid Transfer Protein / Mycoplasma pneumoniae
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.52 Å
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
DepositionMay 15, 2024-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50307.png

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Map

FileDownload / File: emd_50307.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.67 Å/pix.
x 256 pix.
= 428.544 Å		1.67 Å/pix.
x 256 pix.
= 428.544 Å		1.67 Å/pix.
x 256 pix.
= 428.544 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.674 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.114
Minimum - Maximum-0.22949035 - 0.45509738
Average (Standard dev.)-0.0005314877 (±0.012748523)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 428.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50307_msk_1.map
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Half map: #1

Fileemd_50307_half_map_1.map
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Half map: #2

Fileemd_50307_half_map_2.map
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Sample components

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Entire : Mycoplasma pneumoniae protein P116 fragment spanning amino acids ...

EntireName: Mycoplasma pneumoniae protein P116 fragment spanning amino acids 246-818 (dimer in empty state)
Components
  • Complex: Mycoplasma pneumoniae protein P116 fragment spanning amino acids 246-818 (dimer in empty state)

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Supramolecule #1: Mycoplasma pneumoniae protein P116 fragment spanning amino acids ...

SupramoleculeName: Mycoplasma pneumoniae protein P116 fragment spanning amino acids 246-818 (dimer in empty state)
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
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 145945
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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