4M63

Crystal Structure of a Filament-Like Actin Trimer Bound to the Bacterial Effector VopL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.748 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Bacterial Effector VopL Organizes Actin into Filament-like Structures.

Zahm, J.A.Padrick, S.B.Chen, Z.Pak, C.W.Yunus, A.A.Henry, L.Tomchick, D.R.Chen, Z.Rosen, M.K.

(2013) Cell 155: 423-434

  • DOI: 10.1016/j.cell.2013.09.019

  • PubMed Abstract: 
  • VopL is an effector protein from Vibrio parahaemolyticus that nucleates actin filaments. VopL consists of a VopL C-terminal domain (VCD) and an array of three WASP homology 2 (WH2) motifs. Here, we report the crystal structure of the VCD dimer bound ...

    VopL is an effector protein from Vibrio parahaemolyticus that nucleates actin filaments. VopL consists of a VopL C-terminal domain (VCD) and an array of three WASP homology 2 (WH2) motifs. Here, we report the crystal structure of the VCD dimer bound to actin. The VCD organizes three actin monomers in a spatial arrangement close to that found in the canonical actin filament. In this arrangement, WH2 motifs can be modeled into the binding site of each actin without steric clashes. The data suggest a mechanism of nucleation wherein VopL creates filament-like structures, organized by the VCD with monomers delivered by the WH2 array, that can template addition of new subunits. Similarities with Arp2/3 complex and formin proteins suggest that organization of monomers into filament-like structures is a general and central feature of actin nucleation.


    Related Citations: 
    • 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


    Organizational Affiliation

    Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T3SS2 effector VopL nucleation of actin polymerization
A, B
241N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Actin-5C
C, D, E
377Drosophila melanogasterMutation(s): 3 
Gene Names: Act5C
Find proteins for P10987 (Drosophila melanogaster)
Go to UniProtKB:  P10987
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
C, D, E
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
C, D, E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.748 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.219 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/84 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 287.759α = 90.00
b = 66.084β = 94.01
c = 103.160γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
PDB_EXTRACTdata extraction
PHASERphasing
SCALEPACKdata scaling
HKL-3000data reduction
HKL-3000data scaling
PHENIXrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2013-11-13
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description