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- EMDB-51635: P116 from Mycoplasma pneumoniae in complex with mild growth suppr... -

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Basic information

Entry
Database: EMDB / ID: EMD-51635
TitleP116 from Mycoplasma pneumoniae in complex with mild growth suppressor monoclonal antibody
Map dataCryo-EM map of P116 protein from Mycoplasma pneumoniae in complex with a monoclonal antibody
Sample
  • Complex: Binary complex of mild growth suppressor monoclonal antibody with P116 protein from Mycoplasma pneumoniae.
    • Protein or peptide: Heavy chain monoclonal antibody
    • Protein or peptide: Light chain monoclonal antibody
    • Protein or peptide: Uncharacterized protein MG075 homolog
Keywordsimmunodominant / cholesterol / essential lipids / transporter / lipid binder / monoclonal antibody / PROTEIN TRANSPORT
Function / homology: / : / P116-like protein / membrane / Uncharacterized protein MG075 homolog
Function and homology information
Biological speciesMycoplasmoides pneumoniae M129 (bacteria) / Mus musculus (house mouse)
Methodsingle 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, 4 items
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, 2024-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51635.png

Downloads & links

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Map

FileDownload / File: emd_51635.map.gz / Format: CCP4 / Size: 506 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of P116 protein from Mycoplasma pneumoniae in complex with a monoclonal antibody
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.48 Å/pix.
x 510 pix.
= 244.8 Å		0.48 Å/pix.
x 510 pix.
= 244.8 Å		0.48 Å/pix.
x 510 pix.
= 244.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.48 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.0018194956 - 2.2119758
Average (Standard dev.)0.0021950628 (±0.035010755)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions510510510
Spacing510510510
CellA=B=C: 244.79999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B

Fileemd_51635_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_51635_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Binary complex of mild growth suppressor monoclonal antibody with...

EntireName: Binary complex of mild growth suppressor monoclonal antibody with P116 protein from Mycoplasma pneumoniae.
Components
  • Complex: Binary complex of mild growth suppressor monoclonal antibody with P116 protein from Mycoplasma pneumoniae.
    • Protein or peptide: Heavy chain monoclonal antibody
    • Protein or peptide: Light chain monoclonal antibody
    • Protein or peptide: Uncharacterized protein MG075 homolog

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Supramolecule #1: Binary complex of mild growth suppressor monoclonal antibody with...

SupramoleculeName: Binary complex of mild growth suppressor monoclonal antibody with P116 protein from Mycoplasma pneumoniae.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)

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Macromolecule #1: Heavy chain monoclonal antibody

MacromoleculeName: Heavy chain monoclonal antibody / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 22.809572 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: QVQLQQPGAE LVKPGASVKL SCKASGYSFI TYWMRWVRQR PGQGLEWIGQ INPSNGHTNY DEKFKDRATL TVDKSSTTAY LQLSSLTSD DSAVYFCARS WEAMDYWGQG TSVTVSSAKT TAPSVYPLAP VCGVTLGCLV KGYFPEPVTL TWNSGSLSSG V HTFPAVLQ ...String:
QVQLQQPGAE LVKPGASVKL SCKASGYSFI TYWMRWVRQR PGQGLEWIGQ INPSNGHTNY DEKFKDRATL TVDKSSTTAY LQLSSLTSD DSAVYFCARS WEAMDYWGQG TSVTVSSAKT TAPSVYPLAP VCGVTLGCLV KGYFPEPVTL TWNSGSLSSG V HTFPAVLQ SDLYTLSSSV TVTSSTWPSQ SITCNVAHPA SSTKVDKKIE PR

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Macromolecule #2: Light chain monoclonal antibody

MacromoleculeName: Light chain monoclonal antibody / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.367701 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: DIVLTQSPAT LSVTPGDSVS LSCRASQGIS NNLHWYQQKS HESPRLLIKY ASQSFSGIPS RFSGSGSGTV FTLTINSVET EDFGVYFCQ QSYSWPIFTF GSGTNLQIKR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN FYPKDINVKW KIDGSERQNG V LNSWTDQD ...String:
DIVLTQSPAT LSVTPGDSVS LSCRASQGIS NNLHWYQQKS HESPRLLIKY ASQSFSGIPS RFSGSGSGTV FTLTINSVET EDFGVYFCQ QSYSWPIFTF GSGTNLQIKR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN FYPKDINVKW KIDGSERQNG V LNSWTDQD SKDSTYSMSS TLTLTKDEYE RHNSYTCEAT HKTSTSPIVK SFNR

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Macromolecule #3: Uncharacterized protein MG075 homolog

MacromoleculeName: Uncharacterized protein MG075 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Molecular weightTheoretical: 91.165898 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: QPAAATRITV ENGTDKLVNY KSSPQQLFLA KNALKDKLQG EFDKFLSDAK AFPALTADLQ EWVDQQLFNP NQSFFDLSAP RSNFTLSSD KKASLDFIFR FTNFTESVQL LKLPEGVSVV VDSKQSFDYY VNASAQKLLV LPLSLPDYTL GLNYMFDHIT L NGKVVNKF ...String:
QPAAATRITV ENGTDKLVNY KSSPQQLFLA KNALKDKLQG EFDKFLSDAK AFPALTADLQ EWVDQQLFNP NQSFFDLSAP RSNFTLSSD KKASLDFIFR FTNFTESVQL LKLPEGVSVV VDSKQSFDYY VNASAQKLLV LPLSLPDYTL GLNYMFDHIT L NGKVVNKF SFNPFKTNLN LAFSNVYNGV DVFEAQKNLV GKGKYLNTHV KAEDVKKDVN ANIKNQFDIA KIIAELMGKA LK EFGNQQE GQPLSFLKVM DKVKEDFEKL FNLVRPGLGK FVKDLIQSSS QAENKITVYK LIFDNKKTIL NLLKELSIPE LNS SLGLVD VLFDGITDSD GLYERLQSFK DLIVPAVKTN EKTAALSPLI EELLTQKDTY VFDLIQKHKG ILTNLLKNFL ADFQ KSTPF MADQVAIFTE LFDNEGAFDL FGEADFVDKI AELFLTKRTV KNGEKIETKD SLLVTSLKSL LGEKVAALGD LLDSY IFKN ELLNRSVEVA KAEAKDTKGA TDYKKEQAKA LKKLFKHIGE NTLSKTNLDK ITLKEVKNTE NVELEETETT LKVKKL DVE YKVELGNFEI KNGLIKAMLE FLPDTKDLET TLDKLLFKGE SYKAMKDKYI KEGFPGYGWA KGVVPGAFES IENTFKS AI DKTKSIRDLF GDMLFGNDLS SVKETDSFIT LGGSFDIKYG GENLNVLPAY YSLINSEIGY QIIGVDTTID ATKVKVEL K NKEYKGKSPA INGQVKLSQS FFNVWTNMFD SITKQIFQKK YEFKDNIQVF ARNEDNTSRL ELDISDPEQR VIPFAFVDG FGIQLKAVD

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

Concentration0.25 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClSODIUM CHLORIDE
20.0 mMC4H12ClNO3TRIS-HCL
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 7.24 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8a9a

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 412947
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4)

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Atomic model buiding 1

Initial modelPDB ID:

8a9a


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9gvg:
P116 from Mycoplasma pneumoniae in complex with mild growth suppressor monoclonal antibody

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