5JUH

Crystal structure of C-terminal domain (RV) of MpAFP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.125 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a 1.5-MDa adhesin that binds its Antarctic bacterium to diatoms and ice.

Guo, S.Stevens, C.A.Vance, T.D.R.Olijve, L.L.C.Graham, L.A.Campbell, R.L.Yazdi, S.R.Escobedo, C.Bar-Dolev, M.Yashunsky, V.Braslavsky, I.Langelaan, D.N.Smith, S.P.Allingham, J.S.Voets, I.K.Davies, P.L.

(2017) Sci Adv 3: e1701440-e1701440

  • DOI: 10.1126/sciadv.1701440
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial adhesins are modular cell-surface proteins that mediate adherence to other cells, surfaces, and ligands. The Antarctic bacterium Marinomonas primoryensis uses a 1.5-MDa adhesin comprising over 130 domains to position it on ice at the top of ...

    Bacterial adhesins are modular cell-surface proteins that mediate adherence to other cells, surfaces, and ligands. The Antarctic bacterium Marinomonas primoryensis uses a 1.5-MDa adhesin comprising over 130 domains to position it on ice at the top of the water column for better access to oxygen and nutrients. We have reconstructed this 0.6-μm-long adhesin using a "dissect and build" structural biology approach and have established complementary roles for its five distinct regions. Domains in region I (RI) tether the adhesin to the type I secretion machinery in the periplasm of the bacterium and pass it through the outer membrane. RII comprises ~120 identical immunoglobulin-like β-sandwich domains that rigidify on binding Ca2+ to project the adhesion regions RIII and RIV into the medium. RIII contains ligand-binding domains that join diatoms and bacteria together in a mixed-species community on the underside of sea ice where incident light is maximal. RIV is the ice-binding domain, and the terminal RV domain contains several "repeats-in-toxin" motifs and a noncleavable signal sequence that target proteins for export via the type I secretion system. Similar structural architecture is present in the adhesins of many pathogenic bacteria and provides a guide to finding and blocking binding domains to weaken infectivity.


    Organizational Affiliation

    Protein Function Discovery Group and Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antifreeze protein
A
203Marinomonas primoryensisMutation(s): 0 
Find proteins for A1YIY3 (Marinomonas primoryensis)
Go to UniProtKB:  A1YIY3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.125 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 34.960α = 90.00
b = 43.340β = 90.00
c = 78.840γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-05-10 
  • Released Date: 2017-07-19 
  • Deposition Author(s): Guo, S.

Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanada--

Revision History 

  • Version 1.0: 2017-07-19
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence