6RJ1 | pdb_00006rj1

N-Domain P40/P90 Mycoplasma pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb6RJ1/pdb

• Classification: CELL ADHESION
• Organism(s): Mycoplasmoides pneumoniae M129
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-04-25 Released: 2020-11-04 
• Deposition Author(s): Vizarraga, D., Aparicio, D., Illanes, R., Fita, I.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.234 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

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

• PubMed: 33057023 
• DOI: https://doi.org/10.1038/s41467-020-18777-y
• Primary Citation 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.

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Organizational Affiliation: 
• Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain.
Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
Graduate School of Science, Osaka City University, Osaka, 558-8585, Japan.
EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain.
Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, 08208, Sabadell, Spain.
Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
Departament de Microbiologia, Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, 08208, Sabadell, Spain.
Departament de Microbiologia, Hospital Universitari Vall d´Hebron, Universitat Autònoma de Barcelona, 08035, Barcelona, Spain.
Buchmann Institute for Molecular Life Sciences, Max-von-Laue Str. 15, 60438, Frankfurt, Germany.
Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan.
RIKEN Center for Biosystems Dynamics Research and SPring-8 Center, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
Graduate School of Science, Osaka City University, Osaka, 558-8585, Japan. [e-mail].
The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, 558-8585, Japan. [e-mail].
Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 208.65 kDa 
• Atom Count: 12,623 
• Modeled Residue Count: 1,618 
• Deposited Residue Count: 1,952 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mgp-operon protein 3	A, B	976	Mycoplasmoides pneumoniae M129	Mutation(s): 0  Gene Names: MPN_142, MP012
UniProt
Find proteins for Q50341 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50341  Go to UniProtKB:  Q50341

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.234 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.796	α = 90
b = 114.434	β = 90
c = 165.054	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-11-04 
Deposition Author(s): Vizarraga, D., Aparicio, D., Illanes, R., Fita, I.

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Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	--

Revision History  

• 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