3RYL | pdb_00003ryl

Dimerization domain of Vibrio parahemolyticus VopL

• PDB DOI: https://doi.org/10.2210/pdb3RYL/pdb

• Classification: PROTEIN BINDING
• Organism(s): Vibrio parahaemolyticus RIMD 2210633
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-05-11 Released: 2011-08-31 
• Deposition Author(s): Namgoong, S., Dominguez, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.294 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Literature

Mechanism of actin filament nucleation by Vibrio VopL and implications for tandem W domain nucleation.

Namgoong, S., Boczkowska, M., Glista, M.J., Winkelman, J.D., Rebowski, G., Kovar, D.R., Dominguez, R.

(2011) Nat Struct Mol Biol 18: 1060-1067

• PubMed: 21873985 
• DOI: https://doi.org/10.1038/nsmb.2109
• Primary Citation Related Structures: 
  3RYL


• PubMed Abstract: 
  

  Pathogen proteins targeting the actin cytoskeleton often serve as model systems to understand their more complex eukaryotic analogs. We show that the strong actin filament nucleation activity of Vibrio parahaemolyticus VopL depends on its three W domains and on its dimerization through a unique VopL C-terminal domain (VCD). The VCD shows a previously unknown all-helical fold and interacts with the pointed end of the actin nucleus, contributing to the nucleation activity directly and through duplication of the W domain repeat. VopL promotes rapid cycles of filament nucleation and detachment but generally has no effect on elongation. Profilin inhibits VopL-induced nucleation by competing for actin binding to the W domains. Combined, the results suggest that VopL stabilizes a hexameric double-stranded pointed end nucleus. Analysis of hybrid constructs of VopL and the eukaryotic nucleator Spire suggest that Spire may also function as a dimer in cells.

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Organizational Affiliation: 
• Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 54.13 kDa 
• Atom Count: 3,484 
• Modeled Residue Count: 440 
• Deposited Residue Count: 482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protein VPA1370	A, B	241	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 0  Gene Names: VopL, VPA1370
UniProt
Find proteins for Q87GE5 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87GE5  Go to UniProtKB:  Q87GE5

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.294 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.93	α = 90
b = 90.49	β = 90
c = 101.86	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SHELXS	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-31 
Deposition Author(s): Namgoong, S., Dominguez, R.

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 1.1: 2013-06-19
  Changes: Database references
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary