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- EMDB-51410: Mycoplasma pneumoniae protein P116 truncated ectodomain (aa 246-8... -

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Basic information

Entry
Database: EMDB / ID: EMD-51410
TitleMycoplasma pneumoniae protein P116 truncated ectodomain (aa 246-818) dimer in the empty conformation
Map data
Sample
  • Complex: Mycoplasma pneumoniae protein P116 truncated ectodomain (aa 246-818) dimer in the empty conformation
    • Protein or peptide: Mycoplasma pneumoniae protein P116 truncated ectodomain (aa 246-818) dimer in the empty conformation
KeywordsMycoplasma pneumoniae Lipid Transfer Lipid Transport / LIPID BINDING PROTEIN
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.52 Å
AuthorsManger S
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchGRK 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_51410.png

Downloads & links

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Map

FileDownload / File: emd_51410.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

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0618
Minimum - Maximum-0.5610158 - 0.5818584
Average (Standard dev.)-0.00053148763 (±0.015351777)
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_51410_msk_1.map
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Half map: #1

Fileemd_51410_half_map_1.map
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Half map: #2

Fileemd_51410_half_map_2.map
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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) dimer in the empty conformation
Components
  • Complex: Mycoplasma pneumoniae protein P116 truncated ectodomain (aa 246-818) dimer in the empty conformation
    • Protein or peptide: Mycoplasma pneumoniae protein P116 truncated ectodomain (aa 246-818) dimer 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) dimer 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 truncated ectodomain (aa 246-8...

MacromoleculeName: Mycoplasma pneumoniae protein P116 truncated ectodomain (aa 246-818) dimer 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 EGQPLSFLK VMDKVKEDFE KLFNLVRPGL GKFVKDLIQS SSQAENKITV YKLIFDNKKT I LNLLKELS IPELNSSLGL VDVLFDGITD SDGLYERLQS FKDLIVPAVK ...String:
GVDVFEAQKN LVGKGKYLNT HVKAEDVKKD VNANIKNQFD IAKIIAELMG KALKEFGNQQ EGQPLSFLK VMDKVKEDFE KLFNLVRPGL GKFVKDLIQS SSQAENKITV YKLIFDNKKT I LNLLKELS IPELNSSLGL VDVLFDGITD SDGLYERLQS FKDLIVPAVK TNEKTAALSP LI EELLTQK DTYVFDLIQK HKGILTNLLK NFLADFQKST PFMADQVAIF TELFDNEGAF DLF GEADFV DKIAELFLTK RTVKNGEKIE TKDSLLVTSL KSLLGEKVAA LGDLLDSYIF KNEL LNRSV EVAKAEAKDT KGATDYKKEQ AKALKKLFKH IGENTLSKTN LDKITLKEVK NTENV ELEE TETTLKVKKL DVEYKVELGN FEIKNGLIKA MLEFLPDTKD LETTLDKLLF KGESYKAMKD KYIKEGFPGY GWAKGVVPGA FESIENTFKS AIDKTKSIRD LFGDMLFGND LSSVKETDSF ITLGGSFDIK YGGENLNVLP AYYSLINSEI GYQIIGVDTT IDATKVKVEL KNKEYKGKSP AINGQVKLSQ SFFNVWTNMF DSITKQIFQ

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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) / 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: 1650962
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: 6.52 Å / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 145945
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)

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