9GVG | pdb_00009gvg

P116 from Mycoplasma pneumoniae in complex with mild growth suppressor monoclonal antibody


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9GVG

This is version 1.0 of the entry. See complete history

Literature

Sources of essential lipids for Mycoplasma pneumoniae via P116 to target liver and atherosclerotic lesions.

Vizarraga, D.Marcos, M.Rotllan, N.Martin, J.Santos, D.Camacho, M.Soto, B.Velasco-Reniu, L.Guerra, P.Pareja, F.Collantes, M.Wu, W.Rodriguez-Arce, I.Serrano, L.Pinol, J.Fita, I.Escola-Gil, J.C.

(2025) Nat Commun 16: 11159-11159

  • DOI: https://doi.org/10.1038/s41467-025-66129-5
  • Primary Citation Related Structures: 
    9GVG

  • PubMed Abstract: 

    Mycoplasma pneumoniae (MPN) is a bacterial pathogen that primarily causes atypical pneumonia. It cannot synthesize certain essential lipids and therefore relies on the host for their acquisition to survive. MPN has been detected in increased amounts within ruptured atherosclerotic plaques. In this work, we show that the protein P116 facilitates cholesterol acquisition from LDL, HDL and various cell types. Targeting P116's C-terminal domain with a monoclonal antibody inhibits cholesterol acquisition and bacterial growth in vitro. Phase contrast epifluorescence microscopy of human arteries reveals that this antibody blocks MPN binding to atherosclerotic lesions ex vivo. Additionally, an MPN chassis injected into hyperlipidemic female mice localizes to the liver and atherosclerotic plaques. Here, we report that P116 plays a role in extracting essential lipids from lipoproteins and host cells and regulates MPN localization to atheromatous plaques. The study highlights MPN's potential as a tool for targeting atherosclerotic lesions and fatty liver.


  • Organizational Affiliation
    • Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Spain.

Macromolecule Content 

  • Total Structure Weight: 228.51 kDa 
  • Atom Count: 10,018 
  • Modeled Residue Count: 1,278 
  • Deposited Residue Count: 2,040 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain monoclonal antibodyA [auth H]210Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain monoclonal antibodyB [auth L]212Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized protein MG075 homologC [auth P],
D [auth A]
809Mycoplasmoides 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
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONPHENIX
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainBeca Margarita Salas
Spanish Ministry of Science, Innovation, and UniversitiesSpainBIO2017-84166-R
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2021-125632OB-C22
Ministerio de Ciencia e Innovacion (MCIN)SpainPID2021-125632OB-C21

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release