6TM0

N-Domain P40/P90 Mycoplasma pneumoniae complexed with 6'SL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Immunodominant proteins P1 and P40/P90 from human pathogen Mycoplasma pneumoniae.

Vizarraga, D.Kawamoto, A.Matsumoto, U.Illanes, R.Perez-Luque, R.Martin, J.Mazzolini, R.Bierge, P.Pich, O.Q.Espasa, M.Sanfeliu, I.Esperalba, J.Fernandez-Huerta, M.Scheffer, M.P.Pinyol, J.Frangakis, A.S.Lluch-Senar, M.Mori, S.Shibayama, K.Kenri, T.Kato, T.Namba, K.Fita, I.Miyata, M.Aparicio, D.

(2020) Nat Commun 11: 5188-5188

  • DOI: https://doi.org/10.1038/s41467-020-18777-y
  • Primary Citation of Related Structures:  
    6RC9, 6RJ1, 6TLZ, 6TM0, 7BWM

  • PubMed Abstract: 

    Mycoplasma pneumoniae is a bacterial human pathogen that causes primary atypical pneumonia. M. pneumoniae motility and infectivity are mediated by the immunodominant proteins P1 and P40/P90, which form a transmembrane adhesion complex. Here we report the structure of P1, determined by X-ray crystallography and cryo-electron microscopy, and the X-ray structure of P40/P90. Contrary to what had been suggested, the binding site for sialic acid was found in P40/P90 and not in P1. Genetic and clinical variability concentrates on the N-terminal domain surfaces of P1 and P40/P90. Polyclonal antibodies generated against the mostly conserved C-terminal domain of P1 inhibited adhesion of M. pneumoniae, and serology assays with sera from infected patients were positive when tested against this C-terminal domain. P40/P90 also showed strong reactivity against human infected sera. The architectural elements determined for P1 and P40/P90 open new possibilities in vaccine development against M. pneumoniae infections.


  • Organizational Affiliation

    Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mgp-operon protein 3
A, B
976Mycoplasmoides pneumoniae M129Mutation(s): 0 
Gene Names: MPN_142MP012
UniProt
Find proteins for Q50341 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore Q50341 
Go to UniProtKB:  Q50341
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ50341
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
C, D
3N/A
Glycosylation Resources
GlyTouCan:  G28868ZC
GlyCosmos:  G28868ZC
GlyGen:  G28868ZC
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.331α = 90
b = 107.38β = 90.07
c = 160.451γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing
autoXDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpain--

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2020-11-18
    Changes: Structure summary
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description