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- EMDB-19402: Single-particle cryo-EM of Mycoplasma pneumoniae adhesin P1 compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-19402
TitleSingle-particle cryo-EM of Mycoplasma pneumoniae adhesin P1 complexed with the anti-adhesive Fab fragment.
Map data
Sample
  • Complex: Mycoplasma pneumoniae adhesin P1 complexed with the anti-adhesive Fab fragment.
    • Complex: Adhesin P1
      • Protein or peptide: Adhesin P1
    • Complex: Anti-adhesive Fab fragment
      • Protein or peptide: Light Chain Fab
      • Protein or peptide: Heavy Chain Fab
  • Ligand: water
KeywordsAdhesin / Mycoplasma pneumoniae / Sialic acid / Adhesion / CELL ADHESION
Function / homology
Function and homology information


attachment organelle / adhesion of symbiont to microvasculature / cell projection / cell surface / membrane / plasma membrane
Similarity search - Function
Adhesin P1, C-terminal domain / Adhesin P1, N-terminal / Adhesin P1 / Mycoplasma adhesin P1, C-terminal / Mycoplasma adhesin P1, N-terminal
Similarity search - Domain/homology
Biological speciesMycoplasmoides pneumoniae M129 (bacteria) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsVizarraga D / Kawamoto A / Marcos-Silva M / Fita I / Miyata M / Pinyol J / Namba K / Kenri T
Funding support Spain, Japan, 2 items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2021-125632OB-C22, PID2021-125632OB-C21 Spain
Ministry of Education, Culture, Sports, Science and Technology (Japan)22K07063 Japan
CitationJournal: PLoS Pathog / Year: 2025
Title: Dynamics of the adhesion complex of the human pathogens Mycoplasma pneumoniae and Mycoplasma genitalium.
Authors: David Vizarraga / Akihiro Kawamoto / Marina Marcos-Silva / Jesús Martín / Fumiaki Makino / Tomoko Miyata / Jorge Roel-Touris / Enrique Marcos / Oscar Q Pich / David Aparicio / Ignacio Fita ...Authors: David Vizarraga / Akihiro Kawamoto / Marina Marcos-Silva / Jesús Martín / Fumiaki Makino / Tomoko Miyata / Jorge Roel-Touris / Enrique Marcos / Oscar Q Pich / David Aparicio / Ignacio Fita / Makoto Miyata / Jaume Piñol / Keiichi Namba / Tsuyoshi Kenri /
Abstract: Mycoplasma pneumoniae and Mycoplasma genitalium are bacterial wall-less human pathogens and the causative agents of respiratory and reproductive tract infections. Infectivity, gliding motility and ...Mycoplasma pneumoniae and Mycoplasma genitalium are bacterial wall-less human pathogens and the causative agents of respiratory and reproductive tract infections. Infectivity, gliding motility and adhesion of these mycoplasmas to host cells are mediated by orthologous adhesin proteins forming a transmembrane adhesion complex that binds to sialylated oligosaccharides human cell ligands. Here we report the cryo-EM structure of M. pneumoniae P1 adhesin bound to the Fab fragment of monoclonal antibody P1/MCA4, which stops gliding and induces detachment of motile cells. The epitope of P1/MCA4 involves residues only from the small C-domain of P1. This epitope is accessible to antibodies only in the "closed conformation" of the adhesion complex and is not accessible in the "open" conformation, when the adhesion complex is ready for attachment to sialylated oligosaccharides. Polyclonal antibodies generated against the large N-domain of P1 or against the whole ectodomain of P40/P90 have little or no effects on adhesion or motility. Moreover, mutations in the highly conserved Engelman motifs found in the transmembrane helix of M. genitalium P110 adhesin also alter adhesion and motility. These results show that antibodies directed to the C-domain of P1 hinder the large conformational rearrangements in this domain required to alternate between the "open" and "closed" conformations of the adhesion complex. Since transition between both conformations is essential to complete the attachment/detachment cycle of the adhesion complex, interfering with the gliding of mycoplasma cells and providing a new potential target to confront M. pneumoniae and M. genitalium infections.
History
DepositionJan 12, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19402.png

Downloads & links

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Map

FileDownload / File: emd_19402.map.gz / Format: CCP4 / Size: 202.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.5 Å/pix.
x 376 pix.
= 188. Å		0.5 Å/pix.
x 376 pix.
= 188. Å		0.5 Å/pix.
x 376 pix.
= 188. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.010646092 - 0.027007872
Average (Standard dev.)0.00009653149 (±0.0011875686)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions376376376
Spacing376376376
CellA=B=C: 188.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_19402_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19402_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mycoplasma pneumoniae adhesin P1 complexed with the anti-adhesive...

EntireName: Mycoplasma pneumoniae adhesin P1 complexed with the anti-adhesive Fab fragment.
Components
  • Complex: Mycoplasma pneumoniae adhesin P1 complexed with the anti-adhesive Fab fragment.
    • Complex: Adhesin P1
      • Protein or peptide: Adhesin P1
    • Complex: Anti-adhesive Fab fragment
      • Protein or peptide: Light Chain Fab
      • Protein or peptide: Heavy Chain Fab
  • Ligand: water

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Supramolecule #1: Mycoplasma pneumoniae adhesin P1 complexed with the anti-adhesive...

SupramoleculeName: Mycoplasma pneumoniae adhesin P1 complexed with the anti-adhesive Fab fragment.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Fab fragment from a monoclonal antibody that binds to the C-terminal domain of the P1 adhesin of Mycoplasma pneumoniae, interfering with its adhesion to sialic acids.
Molecular weightTheoretical: 200 KDa

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Supramolecule #2: Adhesin P1

SupramoleculeName: Adhesin P1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)

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Supramolecule #3: Anti-adhesive Fab fragment

SupramoleculeName: Anti-adhesive Fab fragment / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Adhesin P1

MacromoleculeName: Adhesin P1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Molecular weightTheoretical: 158.195531 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: NAINPRLTPW TYRNTSFSSL PLTGENPGAW ALVRDNSAKG ITAGSGSQQT TYDPTRTEAA LTASTTFALR RYDLAGRALY DLDFSKLNP QTPTRDQTGQ ITFNPFGGFG LSGAAPQQWN EVKNKVPVEV AQDPSNPYRF AVLLVPRSVV YYEQLQRGLG L PQQRTESG ...String:
NAINPRLTPW TYRNTSFSSL PLTGENPGAW ALVRDNSAKG ITAGSGSQQT TYDPTRTEAA LTASTTFALR RYDLAGRALY DLDFSKLNP QTPTRDQTGQ ITFNPFGGFG LSGAAPQQWN EVKNKVPVEV AQDPSNPYRF AVLLVPRSVV YYEQLQRGLG L PQQRTESG QNTSTTGAMF GLKVKNAEAD TAKSNEKLQG AEATGSSTTS GSGQSTQRGG SSGDTKVKAL KIEVKKKSDS ED NGQLQLE KNDLANAPIK RSEESGQSVQ LKADDFGTAL SSSGSGGNSN PGSPTPWRPW LATEQIHKDL PKWSASILIL YDA PYARNR TAIDRVDHLD PKAMTANYPP SWRTPKWNHH GLWDWKARDV LLQTTGFFNP RRHPEWFDGG QTVADNEKTG FDVD NSENT KQGFQKEADS DKSAPIALPF EAYFANIGNL TWFGQALLVF GGNGHVTKSA HTAPLSIGVF RVRYNATGTS ATVTG WPYA LLFSGMVNKQ TDGLKDLPFN NNRWFEYVPR MAVAGAKFVG RELVLAGTIT MGDTATVPRL LYDELESNLN LVAQGQ GLL REDLQLFTPY GWANRPDLPI GAWSSSSSSS HNAPYYFHNN PDWQDRPIQN VVDAFIKPWE DKNGKDDAKY IYPYRYS GM WAWQVYNWSN KLTDQPLSAD FVNENAYQPN SLFAAILNPE LLAALPDKVK YGKENEFAAN EYERFNQKLT VAPTQGTN W SHFSPTLSRF STGFNLVGSV LDQVLDYVPW IGNGYRYGNN HRGVDDITAP QTSAGSSSGI STNTSGSRSF LPTFSNIGV GLKANVQATL GGSQTMITGG SPRRTLDQAN LQLWTGAGWR NDKASSGQSD ENHTKFTSAT GMDQQGQSGT SAGNPDSLKQ DNISKSGDS LTTQDGNAID QQEATNYTNL PPNLTPTADW PNALSFTNKN NAQRAQLFLR GLLGSIPVLV NRSGSDSNKF Q ATDQKWSY TDLHSDQTKL NLPAYGEVNG LLNPALVETY FGNTRAGGSG SNTTSSPGIG FKIPEQNNDS KATLITPGLA WT PQDVGNL VVSGTTVSFQ LGGWLVTFTD FVKPRAGYLG LQLTGLDASD ATQRALIWAP RPWAAFRGSW VNRLGRVESV WDL KGVWAD QAQSDSQGST TTATRNALPE HPNALAFQVS VVEASAYKPN TSSGQTQSTN SSPYLHLVKP KKVTQSDKLD DDLK NLLDP NQVRTKLRQS FGTDHSTQPQ PQSLKTTTPV FGTSSGNLSS VLSGGGAGGG SSGSGQSGVD LSPVEKVSGW LVGQL PSTS DGNTSSTNNL APNTNTGNDV VGVGRLSESN AAKMNDDVDG IVRTPLAELL DGEGQTADTG PQSVKFKSPD QIDFNR LFT HPVTDLFDPV TMLVYDQYIP LFIDIPASVN PKMVRLKVLS FDTNEQSLGL RLEFFKPDQD TQPNNNVQVN PNNGDFL PL LTASSQGPQT LFSPF

UniProtKB: Adhesin P1

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Macromolecule #2: Light Chain Fab

MacromoleculeName: Light Chain Fab / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.149861 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VLMTQTPLSL PVSLGDQASI SCRFSQTIVH SNGATYLEWY LQRPGQSPKL LIYKVSNRFS GVPDRFSGSG SGTDFTLKIS RVEAEDLGV YYCFQGSHVP WTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT ...String:
VLMTQTPLSL PVSLGDQASI SCRFSQTIVH SNGATYLEWY LQRPGQSPKL LIYKVSNRFS GVPDRFSGSG SGTDFTLKIS RVEAEDLGV YYCFQGSHVP WTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT DQDSKDSTYS MSSTLTLTKD EYERHNSYTC EATHKTSTSP IVKSFNRNEC

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Macromolecule #3: Heavy Chain Fab

MacromoleculeName: Heavy Chain Fab / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.88373 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EVQLQQSGPE LVKPGTSMKI SCKASGYSFT GYTMNWVKQS HGKSLEWIGL INPYNGGTNY NQKFRGTATL TVDKSSSTAY MELLSLTSE DSAVYYCARS NYAYDLLMDY WGQGTSVTVS SAKTTPPSVY PLAPGSAAQT NSMVTLGCLV KGYFPEPVTV T WNSGSLSS ...String:
EVQLQQSGPE LVKPGTSMKI SCKASGYSFT GYTMNWVKQS HGKSLEWIGL INPYNGGTNY NQKFRGTATL TVDKSSSTAY MELLSLTSE DSAVYYCARS NYAYDLLMDY WGQGTSVTVS SAKTTPPSVY PLAPGSAAQT NSMVTLGCLV KGYFPEPVTV T WNSGSLSS GVHTFPAVLQ SDLYTLSSSV TVPSSTWPSE TVTCNVAHPA SSTKVDKKIV PRDC

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 269 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6rc9

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4312408
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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