6R41

Structure of P110 from Mycoplasma genitalium complexed with 3'SL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

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This is version 2.0 of the entry. See complete history


Literature

Mycoplasma genitalium adhesin P110 binds sialic-acid human receptors.

Aparicio, D.Torres-Puig, S.Ratera, M.Querol, E.Pinyol, J.Pich, O.Q.Fita, I.

(2018) Nat Commun 9: 4471

  • DOI: 10.1038/s41467-018-06963-y
  • Primary Citation of Related Structures:  
    5OX7, 6R3T, 6R41, 6R43

  • PubMed Abstract: 
  • Adhesion of pathogenic bacteria to target cells is a prerequisite for colonization and further infection. The main adhesins of the emerging sexually transmitted pathogen Mycoplasma genitalium, P140 and P110, interact to form a Nap complex anchored to the cell membrane ...

    Adhesion of pathogenic bacteria to target cells is a prerequisite for colonization and further infection. The main adhesins of the emerging sexually transmitted pathogen Mycoplasma genitalium, P140 and P110, interact to form a Nap complex anchored to the cell membrane. Herein, we present the crystal structures of the extracellular region of the virulence factor P110 (916 residues) unliganded and in complex with sialic acid oligosaccharides. P110 interacts only with the neuraminic acid moiety of the oligosaccharides and experiments with human cells demonstrate that these interactions are essential for mycoplasma cytadherence. Additionally, structural information provides a deep insight of the P110 antigenic regions undergoing programmed variation to evade the host immune response. These results enlighten the interplay of M. genitalium with human target cells, offering new strategies to control mycoplasma infections.


    Organizational Affiliation

    Instituto de Biología Molecular de Barcelona (IBMB-CSIC) and Maria de Maeztu Unit of Excellence, Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain. ifrcri@ibmb.csic.es.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mgp-operon protein 3A916Mycoplasma genitalium G37Mutation(s): 0 
Gene Names: MG192
UniProt
Find proteins for P22747 (Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195))
Explore P22747 
Go to UniProtKB:  P22747
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranoseB2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G30207PZ
GlyCosmos:  G30207PZ
GlyGen:  G30207PZ
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC (Subject of Investigation/LOI)
Query on BGC

Download Ideal Coordinates CCD File 
D [auth A]beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
C [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.026α = 90
b = 151.569β = 90
c = 176.548γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2019-03-21 
  • Released Date: 2019-05-08 
  • Deposition Author(s): Aparicio, D., Fita, I.
  • This entry supersedes: 5MZ9

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary