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- EMDB-51408: Mycoplasma pneumoniae protein P116 ectodomain in the empty confor... -

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Basic information

Entry
Database: EMDB / ID: EMD-51408
TitleMycoplasma pneumoniae protein P116 ectodomain in the empty conformation
Map data
Sample
  • Complex: Mycoplasma pneumoniae protein P116 ectodomain in the empty conformation
    • Protein or peptide: Mycoplasma pneumoniae protein P116 ectodomain in the empty conformation
KeywordsMycoplasma pneumoniae Lipid Transfer Lipid Transport / LIPID BINDING PROTEIN
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.36 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_51408.png

Downloads & links

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Map

FileDownload / File: emd_51408.map.gz / Format: CCP4 / Size: 512 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.)
0.83 Å/pix.
x 512 pix.
= 425.472 Å		0.83 Å/pix.
x 512 pix.
= 425.472 Å		0.83 Å/pix.
x 512 pix.
= 425.472 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0569
Minimum - Maximum-1.1955479 - 1.2438228
Average (Standard dev.)-0.00005364244 (±0.009339912)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 425.472 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51408_msk_1.map
Projections & Slices
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Half map: #1

Fileemd_51408_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_51408_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Mycoplasma pneumoniae protein P116 ectodomain in the empty confor...

EntireName: Mycoplasma pneumoniae protein P116 ectodomain in the empty conformation
Components
  • Complex: Mycoplasma pneumoniae protein P116 ectodomain in the empty conformation
    • Protein or peptide: Mycoplasma pneumoniae protein P116 ectodomain in the empty conformation

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Supramolecule #1: Mycoplasma pneumoniae protein P116 ectodomain in the empty confor...

SupramoleculeName: Mycoplasma pneumoniae protein P116 ectodomain in the empty conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)

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Macromolecule #1: Mycoplasma pneumoniae protein P116 ectodomain in the empty confor...

MacromoleculeName: Mycoplasma pneumoniae protein P116 ectodomain 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: NKTHQVEHES EQSDFQDIRF GLNSVKLPKA QPAAATRITV ENGTDKLVNY KSSPQQLFLA KNALKDKLQG EFDKFLSDAK AFPALTADLQ EWVDQQLFNP NQSFFDLSAP RSNFTLSSDK KASLDFIFRF TNFTESVQLL KLPEGVSVVV DSKQSFDYYV NASAQKLLVL ...String:
NKTHQVEHES EQSDFQDIRF GLNSVKLPKA QPAAATRITV ENGTDKLVNY KSSPQQLFLA KNALKDKLQG EFDKFLSDAK AFPALTADLQ EWVDQQLFNP NQSFFDLSAP RSNFTLSSDK KASLDFIFRF TNFTESVQLL KLPEGVSVVV DSKQSFDYYV NASAQKLLVL PLSLPDYTLG LNYMFDHITL NGKVVNKFSF NPFKTNLNLA FSNVYNGVDV FEAQKNLVGK GKYLNTHVKA EDVKKDVNAN IKNQFDIAKI IAELMGKALK EFGNQQEGQP LSFLKVMDKV KEDFEKLFNL VRPGLGKFVK DLIQSSSQAE NKITVYKLIF DNKKTILNLL KELSIPELNS SLGLVDVLFD GITDSDGLYE RLQSFKDLIV PAVKTNEKTA ALSPLIEELL TQKDTYVFDL IQKHKGILTN LLKNFLADFQ KSTPFMADQV AIFTELFDNE GAFDLFGEAD FVDKIAELFL TKRTVKNGEK IETKDSLLVT SLKSLLGEKV AALGDLLDSY IFKNELLNRS VEVAKAEAKD TKGATDYKKE QAKALKKLFK HIGENTLSKT NLDKITLKEV KNTENVELEE TETTLKVKKL DVEYKVELGN FEIKNGLIKA MLEFLPDTKD LETTLDKLLF KGESYKAMKD KYIKEGFPGY GWAKGVVPGA FESIENTFKS AIDKTKSIRD LFGDMLFGND LSSVKETDSF ITLGGSFDIK YGGENLNVLP AYYSLINSEI GYQIIGVDTT IDATKVKVEL KNKEYKGKSP AINGQVKLSQ SFFNVWTNMF DSITKQIFQK KYEFKDNIQV FARNEDNTSR LELDISDPEQ RVIPFAFVDG FGIQLKAVDK NITKEAGNTE PKSPVIQLYE ALNKEKDQKQ QSKQSPKQLD TKTQLGYLLK LGDNWSKDDY KSLIDDTIIN NNYLEASFNS KITVDRLGIP IDLWLFKIWP KFNLEIPMQG SLQLYSSSVI FPYGIYDTSV QDAAKIVKRL NFTDMGFKLN DPKPNFWFVG FKHHHHH

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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

Concentration0.6 mg/mL
BufferpH: 7.4 / Details: 20 mM Tris, 2 mM CHAPSO
GridModel: C-flat-1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
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: 9736 / 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: 8534957
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 436559
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.5.3)

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