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- PDB-8ror: Single-particle cryo-EM of Mycoplasma pneumoniae adhesin P1 compl... -

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Basic information

Entry
Database: PDB / ID: 8ror
TitleSingle-particle cryo-EM of Mycoplasma pneumoniae adhesin P1 complexed with the anti-adhesive Fab fragment.
Components
  • Adhesin P1
  • Heavy Chain Fab
  • Light Chain Fab
KeywordsCELL ADHESION / Adhesin / Mycoplasma pneumoniae / Sialic acid / 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)
MethodELECTRON MICROSCOPY / single 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, 2items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / em_admin / em_author_list
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Revision 1.1Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Category: citation / citation_author ...citation / citation_author / em_admin / em_author_list
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Adhesin P1
L: Light Chain Fab
H: Heavy Chain Fab


Theoretical massNumber of molelcules
Total (without water)206,2293
Polymers206,2293
Non-polymers00
Water4,846269
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: Protein Adhesin P1 / Attachment protein / Cytadhesin P1


Mass: 158195.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasmoides pneumoniae M129 (bacteria)
Gene: mgpA, MPN_141, MP013 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P11311
#2: Antibody Light Chain Fab


Mass: 24149.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Antibody Heavy Chain Fab


Mass: 23883.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Mycoplasma pneumoniae adhesin P1 complexed with the anti-adhesive Fab fragment.COMPLEXFab 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.#1-#30MULTIPLE SOURCES
2Adhesin P1COMPLEX#11RECOMBINANT
3Anti-adhesive Fab fragmentCOMPLEX#2-#31RECOMBINANT
Molecular weightValue: 0.20 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Mycoplasmoides pneumoniae M129 (bacteria)272634
33Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli BL21(DE3) (bacteria)469008
33Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4312408 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00514292
ELECTRON MICROSCOPYf_angle_d0.66319486
ELECTRON MICROSCOPYf_dihedral_angle_d5.1491920
ELECTRON MICROSCOPYf_chiral_restr0.0432131
ELECTRON MICROSCOPYf_plane_restr0.0052557

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