3SEO | pdb_00003seo

Crystal structure of VopL C terminal domain

• PDB DOI: https://doi.org/10.2210/pdb3SEO/pdb

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


• Deposited: 2011-06-10 Released: 2011-08-31 
• Deposition Author(s): Yu, B., Rosen, M.K., Tomchick, D.R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 
  0.275 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Literature

Mechanism of actin filament nucleation by the bacterial effector VopL.

Yu, B., Cheng, H.C., Brautigam, C.A., Tomchick, D.R., Rosen, M.K.

(2011) Nat Struct Mol Biol 18: 1068-1074

• PubMed: 21873984 
• DOI: https://doi.org/10.1038/nsmb.2110
• Primary Citation Related Structures: 
  3SEO


• PubMed Abstract: 
  

  Vibrio parahaemolyticus protein L (VopL) is an actin nucleation factor that induces stress fibers when injected into eukaryotic host cells. VopL contains three N-terminal Wiskott-Aldrich homology 2 (WH2) motifs and a unique VopL C-terminal domain (VCD). We describe crystallographic and biochemical analyses of filament nucleation by VopL. The WH2 element of VopL does not nucleate on its own and requires the VCD for activity. The VCD forms a U-shaped dimer in the crystal, stabilized by a terminal coiled coil. Dimerization of the WH2 motifs contributes strongly to nucleation activity, as do contacts of the VCD to actin. Our data lead to a model in which VopL stabilizes primarily lateral (short-pitch) contacts between actin monomers to create the base of a two-stranded filament. Stabilization of lateral contacts may be a common feature of actin filament nucleation by WH2-based factors.

---

Organizational Affiliation: 
• Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 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: 53.98 kDa 
• Atom Count: 3,555 
• Modeled Residue Count: 444 
• Deposited Residue Count: 482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VopL C terminal domain protein	A, B	241	Vibrio parahaemolyticus	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

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth B], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free:  0.275 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.18	α = 90
b = 89.851	β = 90
c = 103.007	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-31 
Deposition Author(s): Yu, B., Rosen, M.K., Tomchick, D.R.

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 1.1: 2012-05-23
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Advisory, Refinement description
• Version 1.3: 2024-02-28
  Changes: Advisory, Data collection, Database references, Derived calculations