8A9B

Single Particle cryo-EM of the empty lipid binding protein P116 (MPN213) from Mycoplasma pneumoniae at 4 Angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Essential protein P116 extracts cholesterol and other indispensable lipids for Mycoplasmas.

Sprankel, L.Vizarraga, D.Martin, J.Manger, S.Meier-Credo, J.Marcos, M.Julve, J.Rotllan, N.Scheffer, M.P.Escola-Gil, J.C.Langer, J.D.Pinol, J.Fita, I.Frangakis, A.S.

(2023) Nat Struct Mol Biol 30: 321-329

  • DOI: https://doi.org/10.1038/s41594-023-00922-y
  • Primary Citation of Related Structures:  
    8A9A, 8A9B

  • PubMed 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 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.


  • Organizational Affiliation

    Buchmann Institute for Molecular Life Sciences and Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipid binding protein P116 (MPN213)A [auth B]1,007Mycoplasmoides pneumoniae M129Mutation(s): 0 
Gene Names: MPN_213G07_orf1030MP618
UniProt
Find proteins for P75556 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore P75556 
Go to UniProtKB:  P75556
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP75556
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyFR 1653/14-1
German Research Foundation (DFG)GermanyFR 1653/6-3
German Research Foundation (DFG)GermanyGRK 2566/1

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references