6RUT

Mycoplasma Genitalium Heterodimer Nap Complex (P140-P110 globular)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and mechanism of the Nap adhesion complex from the human pathogen Mycoplasma genitalium.

Aparicio, D.Scheffer, M.P.Marcos-Silva, M.Vizarraga, D.Sprankel, L.Ratera, M.Weber, M.S.Seybert, A.Torres-Puig, S.Gonzalez-Gonzalez, L.Reitz, J.Querol, E.Pinol, J.Pich, O.Q.Fita, I.Frangakis, A.S.

(2020) Nat Commun 11: 2877-2877

  • DOI: https://doi.org/10.1038/s41467-020-16511-2
  • Primary Citation of Related Structures:  
    6RUT, 6S3U, 6YRK

  • PubMed Abstract: 

    Mycoplasma genitalium is a human pathogen adhering to host target epithelial cells and causing urethritis, cervicitis and pelvic inflammatory disease. Essential for infectivity is a transmembrane adhesion complex called Nap comprising proteins P110 and P140. Here we report the crystal structure of P140 both alone and in complex with the N-terminal domain of P110. By cryo-electron microscopy (cryo-EM) and tomography (cryo-ET) we find closed and open Nap conformations, determined at 9.8 and 15 Å, respectively. Both crystal structures and the cryo-EM structure are found in a closed conformation, where the sialic acid binding site in P110 is occluded. By contrast, the cryo-ET structure shows an open conformation, where the binding site is accessible. Structural information, in combination with functional studies, suggests a mechanism for attachment and release of M. genitalium to and from the host cell receptor, in which Nap conformations alternate to sustain motility and guarantee infectivity.


  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mgp-operon protein 3
A, C, E, G
802Mycoplasmoides genitalium G37Mutation(s): 0 
Gene Names: MG192
Membrane Entity: Yes 
UniProt
Find proteins for P22747 (Mycoplasma genitalium (strain ATCC 33530 / DSM 19775 / NCTC 10195 / G37))
Explore P22747 
Go to UniProtKB:  P22747
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22747
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Adhesin P1
B, D, F, H
1,334Mycoplasmoides genitalium G37Mutation(s): 0 
Gene Names: mgpAMG191
Membrane Entity: Yes 
UniProt
Find proteins for P20796 (Mycoplasma genitalium (strain ATCC 33530 / DSM 19775 / NCTC 10195 / G37))
Explore P20796 
Go to UniProtKB:  P20796
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20796
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151α = 90
b = 157.28β = 93.81
c = 192.37γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainMDM-2014-0435

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description