Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 114079.75 
• Atom Count: 7347 
• Residue Count: 1019 
• Unique protein chains: 2

4CI6

Mechanisms of crippling actin-dependent phagocytosis by YopO

• DOI: 10.2210/pdb4CI6/pdb

• Classification: TRANSFERASE/STRUCTURAL PROTEIN
• Organism(s): Spodoptera frugiperda, Yersinia enterocolitica
• Expression System: Escherichia coli
• Mutation(s): 5 


• Deposited: 2013-12-06 Released: 2015-01-28 
• Deposition Author(s): Lee, W.L., Grimes, J.M., Robinson, R.C.

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Experimental Data Snapshot

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

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

• PubMed: 25664724 
• 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-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.

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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
Molecule	Chains	Sequence Length	Organism	Details
ACTIN	A	376	Spodoptera frugiperda	Mutation(s): 0
Find proteins for G3CKA6 (Spodoptera frugiperda) Go to UniProtKB:  G3CKA6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN KINASE YOPO	B	643	Yersinia enterocolitica	Mutation(s): 5  Gene Names: yopO (ypkA) EC: 2.7.11.1
Find proteins for Q93KQ6 (Yersinia enterocolitica) Go to UniProtKB:  Q93KQ6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ATP	A	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 70.799	α = 90.00
b = 121.850	β = 94.87
c = 89.339	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
HKL-2000	data reduction
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-12-06 
• Released Date: 2015-01-28 
• Deposition Author(s): Lee, W.L., Grimes, J.M., Robinson, R.C.

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