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- EMDB-51412: Mycoplasma pneumoniae protein P116 truncated ectodomain (aa 246-8... -

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Basic information

Entry
Database: EMDB / ID: EMD-51412
TitleMycoplasma pneumoniae protein P116 truncated ectodomain (aa 246-818) monomer in the empty conformation
Map data
Sample
  • Complex: Mycoplasma pneumoniae protein P116 truncated ectodomain (aa 246-818) monomer in the empty conformation
    • Protein or peptide: Mycoplasma pneumoniae protein P116 truncated ectodomain (aa 246-818) monomer in the empty conformation
KeywordsMycoplasma pneumoniae Lipid Transfer Lipid Transport / LIPID BINDING PROTEIN
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.3 Å
AuthorsManger S
Funding support Germany, 1 items
OrganizationGrant numberCountry
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
DepositionAug 23, 2024-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51412.png

Downloads & links

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Map

FileDownload / File: emd_51412.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.)
0.84 Å/pix.
x 256 pix.
= 214.272 Å		0.84 Å/pix.
x 256 pix.
= 214.272 Å		0.84 Å/pix.
x 256 pix.
= 214.272 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0338
Minimum - Maximum-0.17445946 - 0.2466409
Average (Standard dev.)-0.00039164256 (±0.010095472)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 214.272 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51412_msk_1.map
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Half map: #1

Fileemd_51412_half_map_1.map
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Half map: #2

Fileemd_51412_half_map_2.map
Projections & Slices
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Sample components

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Entire : Mycoplasma pneumoniae protein P116 truncated ectodomain (aa 246-8...

EntireName: Mycoplasma pneumoniae protein P116 truncated ectodomain (aa 246-818) monomer in the empty conformation
Components
  • Complex: Mycoplasma pneumoniae protein P116 truncated ectodomain (aa 246-818) monomer in the empty conformation
    • Protein or peptide: Mycoplasma pneumoniae protein P116 truncated ectodomain (aa 246-818) monomer in the empty conformation

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Supramolecule #1: Mycoplasma pneumoniae protein P116 truncated ectodomain (aa 246-8...

SupramoleculeName: Mycoplasma pneumoniae protein P116 truncated ectodomain (aa 246-818) monomer in the empty conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Conformation after emptying by detergent treatment
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)

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Macromolecule #1: Mycoplasma pneumoniae protein P116 truncated ectodomain (aa 246-8...

MacromoleculeName: Mycoplasma pneumoniae protein P116 truncated ectodomain (aa 246-818) monomer in the empty conformation
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GVDVFEAQKN LVGKGKYLNT HVKAEDVKKD VNANIKNQFD IAKIIAELMG KALKEFGNQQ EGQPLSFLKV MDKVKEDFEK LFNLVRPGLG KFVKDLIQSS SQAENKITVY KLIFDNKKTI LNLLKELSI PELNSSLGLV DVLFDGITDS DGLYERLQSF KDLIVPAVKT ...String:
GVDVFEAQKN LVGKGKYLNT HVKAEDVKKD VNANIKNQFD IAKIIAELMG KALKEFGNQQ EGQPLSFLKV MDKVKEDFEK LFNLVRPGLG KFVKDLIQSS SQAENKITVY KLIFDNKKTI LNLLKELSI PELNSSLGLV DVLFDGITDS DGLYERLQSF KDLIVPAVKT NEKTAALSPL I EELLTQKD TYVFDLIQKH KGILTNLLKN FLADFQKSTP FMADQVAIFT ELFDNEGAFD LF GEADFVD KIAELFLTKR TVKNGEKIET KDSLLVTSLK SLLGEKVAAL GDLLDSYIFK NEL LNRSVE VAKAEAKDTK GATDYKKEQA KALKKLFKHI GENTLSKTNL DKITLKEVKN TENV ELEET ETTLKVKKLD VEYKVELGNF EIKNGLIKAM LEFLPDTKDL ETTLDKLLFK GESYKAMKDK YIKEGFPGYG WAKGVVPGAF ESIENTFKSA IDKTKSIRDL FGDMLFGNDL SSVKETDSFI TLGGSFDIKY GGENLNVLPA YYSLINSEIG YQIIGVDTTI DATKVKVELK NKEYKGKSPA INGQVKLSQS FFNVWTNMFD SITKQIFQ

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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

Concentration3 mg/mL
BufferpH: 7.4 / Details: 20 mM Tris-HCl. 1 mM CHAPSO
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: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 8002 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6997649
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8a9b


Details: truncated to aa 246-818 compared with PDB 8a9a truncated to aa 246-818
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 1470056
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)

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