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- EMDB-50314: P116 (amino acids 246-818) dimer in the full state -

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Basic information

Entry
Database: EMDB / ID: EMD-50314
TitleP116 (amino acids 246-818) dimer in the full state
Map data
Sample
  • Complex: P116 from Mycoplasma pneumoniae (aa 246-818; full state)
    • Protein or peptide: Uncharacterized protein MG075 homolog
KeywordsLipid Transfer Protein / Mycoplasma pneumoniae / LIPID BINDING PROTEIN
Function / homologymembrane / Uncharacterized protein MG075 homolog
Function and homology information
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.52 Å
AuthorsMager 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_50314.png

Downloads & links

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Map

FileDownload / File: emd_50314.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.)
1.64 Å/pix.
x 256 pix.
= 419.328 Å		1.64 Å/pix.
x 256 pix.
= 419.328 Å		1.64 Å/pix.
x 256 pix.
= 419.328 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.638 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.226
Minimum - Maximum-0.16132881 - 0.77959734
Average (Standard dev.)0.00004181397 (±0.016118696)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 419.328 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50314_msk_1.map
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Half map: #1

Fileemd_50314_half_map_1.map
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Half map: #2

Fileemd_50314_half_map_2.map
Projections & Slices
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Sample components

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Entire : P116 from Mycoplasma pneumoniae (aa 246-818; full state)

EntireName: P116 from Mycoplasma pneumoniae (aa 246-818; full state)
Components
  • Complex: P116 from Mycoplasma pneumoniae (aa 246-818; full state)
    • Protein or peptide: Uncharacterized protein MG075 homolog

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Supramolecule #1: P116 from Mycoplasma pneumoniae (aa 246-818; full state)

SupramoleculeName: P116 from Mycoplasma pneumoniae (aa 246-818; full state)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)

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Macromolecule #1: Uncharacterized protein MG075 homolog

MacromoleculeName: Uncharacterized protein MG075 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Molecular weightTheoretical: 64.38675 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GVDVFEAQKN LVGKGKYLNT HVKAEDVKKD VNANIKNQFD IAKIIAELMG KALKEFGNQQ EGQPLSFLKV MDKVKEDFEK LFNLVRPGL GKFVKDLIQS SSQAENKITV YKLIFDNKKT ILNLLKELSI PELNSSLGLV DVLFDGITDS DGLYERLQSF K DLIVPAVK ...String:
GVDVFEAQKN LVGKGKYLNT HVKAEDVKKD VNANIKNQFD IAKIIAELMG KALKEFGNQQ EGQPLSFLKV MDKVKEDFEK LFNLVRPGL GKFVKDLIQS SSQAENKITV YKLIFDNKKT ILNLLKELSI PELNSSLGLV DVLFDGITDS DGLYERLQSF K DLIVPAVK TNEKTAALSP LIEELLTQKD TYVFDLIQKH KGILTNLLKN FLADFQKSTP FMADQVAIFT ELFDNEGAFD LF GEADFVD KIAELFLTKR TVKNGEKIET KDSLLVTSLK SLLGEKVAAL GDLLDSYIFK NELLNRSVEV AKAEAKDTKG ATD YKKEQA KALKKLFKHI GENTLSKTNL DKITLKEVKN TENVELEETE TTLKVKKLDV EYKVELGNFE IKNGLIKAML EFLP DTKDL ETTLDKLLFK GESYKAMKDK YIKEGFPGYG WAKGVVPGAF ESIENTFKSA IDKTKSIRDL FGDMLFGNDL SSVKE TDSF ITLGGSFDIK YGGENLNVLP AYYSLINSEI GYQIIGVDTT IDATKVKVEL KNKEYKGKSP AINGQVKLSQ SFFNVW TNM FDSITKQIFQ

UniProtKB: Uncharacterized protein MG075 homolog

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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
GridModel: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 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
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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