5U6F | pdb_00005u6f

Bacterial adhesin from Mobiluncus mulieris containing intramolecular disulfide, isopeptide, and ester bond cross-links (space group P21)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.267 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5U6F

This is version 1.2 of the entry. See complete history

Literature

Domain structure and cross-linking in a giant adhesin from the Mobiluncus mulieris bacterium.

Young, P.G.Paynter, J.M.Wardega, J.K.Middleditch, M.J.Payne, L.S.Baker, E.N.Squire, C.J.

(2023) Acta Crystallogr D Struct Biol 79: 971-979

  • DOI: https://doi.org/10.1107/S2059798323007507
  • Primary Citation Related Structures: 
    5U5O, 5U6F

  • PubMed Abstract: 

    Cell-surface proteins known as adhesins enable bacteria to colonize particular environments, and in Gram-positive bacteria often contain autocatalytically formed covalent intramolecular cross-links. While investigating the prevalence of such cross-links, a remarkable example was discovered in Mobiluncus mulieris, a pathogen associated with bacterial vaginosis. This organism encodes a putative adhesin of 7651 residues. Crystallography and mass spectrometry of two selected domains, and AlphaFold structure prediction of the remainder of the protein, were used to show that this adhesin belongs to the family of thioester, isopeptide and ester-bond-containing proteins (TIE proteins). It has an N-terminal domain homologous to thioester adhesion domains, followed by 51 immunoglobulin (Ig)-like domains containing ester- or isopeptide-bond cross-links. The energetic cost to the M. mulieris bacterium in retaining such a large adhesin as a single gene or protein construct suggests a critical role in pathogenicity and/or persistence.


  • Organizational Affiliation
    • School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand.

Macromolecule Content 

  • Total Structure Weight: 31.39 kDa 
  • Atom Count: 2,276 
  • Modeled Residue Count: 288 
  • Deposited Residue Count: 292 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LPXTG-motif cell wall anchor domain protein292Mobiluncus mulierisMutation(s): 0 
UniProt
Find proteins for E0QN07 (Mobiluncus mulieris ATCC 35239)
Explore E0QN07 
Go to UniProtKB:  E0QN07
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE0QN07
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.267 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.548α = 90
b = 51.604β = 101.6
c = 81.206γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-09
    Changes: Structure summary