4CI6

Mechanisms of crippling actin-dependent phagocytosis by YopO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.651 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Yersinia Effector Yopo Uses Actin as Bait to Phosphorylate Proteins that Regulate Actin Polymerization.

Lee, W.L.Grimes, J.M.Robinson, R.C.

(2015) Nat.Struct.Mol.Biol. 22: 248

  • DOI: 10.1038/nsmb.2964

  • PubMed Abstract: 
  • Pathogenic Yersinia species evade host immune systems through the injection of Yersinia outer proteins (Yops) into phagocytic cells. One Yop, YopO, also known as YpkA, induces actin-filament disruption, impairing phagocytosis. Here we describe the X- ...

    Pathogenic Yersinia species evade host immune systems through the injection of Yersinia outer proteins (Yops) into phagocytic cells. One Yop, YopO, also known as YpkA, induces actin-filament disruption, impairing phagocytosis. Here we describe the X-ray structure of Yersinia enterocolitica YopO in complex with actin, which reveals that YopO binds to an actin monomer in a manner that blocks polymerization yet allows the bound actin to interact with host actin-regulating proteins. SILAC-MS and biochemical analyses confirm that actin-polymerization regulators such as VASP, EVL, WASP, gelsolin and the formin diaphanous 1 are directly sequestered and phosphorylated by YopO through formation of ternary complexes with actin. This leads to a model in which YopO at the membrane sequesters actin from polymerization while using the bound actin as bait to recruit, phosphorylate and misregulate host actin-regulating proteins to disrupt phagocytosis.


    Organizational Affiliation

    1] Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore. [2] Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACTIN
A
376Spodoptera frugiperdaN/A
Find proteins for G3CKA6 (Spodoptera frugiperda)
Go to UniProtKB:  G3CKA6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN KINASE YOPO
B
643Yersinia enterocoliticaGene Names: yopO (ypkA)
EC: 2.7.11.1
Find proteins for Q93KQ6 (Yersinia enterocolitica)
Go to UniProtKB:  Q93KQ6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
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: 2.651 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.799α = 90.00
b = 121.850β = 94.87
c = 89.339γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2015-02-11
    Type: Database references
  • Version 1.2: 2015-03-04
    Type: Database references
  • Version 1.3: 2015-03-18
    Type: Database references