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- PDB-9gvg: P116 from Mycoplasma pneumoniae in complex with mild growth suppr... -

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Basic information

Entry
Database: PDB / ID: 9gvg
TitleP116 from Mycoplasma pneumoniae in complex with mild growth suppressor monoclonal antibody
Components
  • Heavy chain monoclonal antibody
  • Light chain monoclonal antibody
  • Uncharacterized protein MG075 homolog
KeywordsPROTEIN TRANSPORT / immunodominant / cholesterol / essential lipids / transporter / lipid binder / monoclonal antibody
Function / homology: / : / P116-like protein / membrane / Uncharacterized protein MG075 homolog
Function and homology information
Biological speciesMus musculus (house mouse)
Mycoplasmoides pneumoniae M129 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.06 Å
AuthorsVizarraga, D. / Marcos Silva, M. / Martin Romero, J. / Guerra, P. / Fita, I. / Pinyol, J.
Funding support Spain, 4items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBeca Margarita Salas Spain
Spanish Ministry of Science, Innovation, and UniversitiesBIO2017-84166-R Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2021-125632OB-C22 Spain
Ministerio de Ciencia e Innovacion (MCIN)PID2021-125632OB-C21 Spain
CitationJournal: Nat Commun / Year: 2025
Title: Sources of essential lipids for Mycoplasma pneumoniae via P116 to target liver and atherosclerotic lesions.
Authors: David Vizarraga / Marina Marcos / Noemi Rotllan / Jesús Martín / David Santos / Mercedes Camacho / Begoña Soto / Lorena Velasco-Reniu / Pablo Guerra / Félix Pareja / María Collantes / ...Authors: David Vizarraga / Marina Marcos / Noemi Rotllan / Jesús Martín / David Santos / Mercedes Camacho / Begoña Soto / Lorena Velasco-Reniu / Pablo Guerra / Félix Pareja / María Collantes / Wanlu Wu / Irene Rodríguez-Arce / Luis Serrano / Jaume Piñol / Ignacio Fita / Joan Carles Escolà-Gil /
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 ...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.
History
DepositionSep 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Heavy chain monoclonal antibody
L: Light chain monoclonal antibody
P: Uncharacterized protein MG075 homolog
A: Uncharacterized protein MG075 homolog


Theoretical massNumber of molelcules
Total (without water)228,5094
Polymers228,5094
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Antibody Heavy chain monoclonal antibody


Mass: 22809.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody Light chain monoclonal antibody


Mass: 23367.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Protein Uncharacterized protein MG075 homolog


Mass: 91165.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasmoides pneumoniae M129 (bacteria)
Gene: MPN_213, G07_orf1030, MP618 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P75556
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Binary complex of mild growth suppressor monoclonal antibody with P116 protein from Mycoplasma pneumoniae.
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSODIUM CHLORIDENaCl1
220 mMTRIS-HCLC4H12ClNO31
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 7.24 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4particle selection
4cryoSPARCv4CTF correction
7PHENIXmodel fitting
9cryoSPARCv4initial Euler assignment
10cryoSPARCv4final Euler assignment
11cryoSPARCv4classification
12PHENIX3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 412947 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingPDB-ID: 8A9A

8a9a


Pdb chain-ID: A / Accession code: 8A9A / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310224
ELECTRON MICROSCOPYf_angle_d0.72513830
ELECTRON MICROSCOPYf_dihedral_angle_d6.0041344
ELECTRON MICROSCOPYf_chiral_restr0.0461565
ELECTRON MICROSCOPYf_plane_restr0.0051763

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