6TLZ

N-Domain P40/P90 Mycoplasma pneumoniae complexed with 3'SL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.279 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.245 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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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
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
C
3N/A
Glycosylation Resources
GlyTouCan:  G91237TK
GlyCosmos:  G91237TK
GlyGen:  G91237TK
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
D
2N/A
Glycosylation Resources
GlyTouCan:  G84224TW
GlyCosmos:  G84224TW
GlyGen:  G84224TW
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SIA (Subject of Investigation/LOI)
Query on SIA

Download Ideal Coordinates CCD File 
E [auth B]N-acetyl-alpha-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.279 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.245 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.212α = 90
b = 107.312β = 90.12
c = 162.013γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing
PDB_EXTRACTdata extraction
xia2data reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SIAClick on this verticalbar to view details

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