1IJJ

THE X-RAY CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN RABBIT SKELETAL MUSCLE ACTIN AND LATRUNCULIN A AT 2.85 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.233 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Polylysine induces an antiparallel actin dimer that nucleates filament assembly: crystal structure at 3.5-A resolution

Bubb, M.R.Govindasamy, L.Yarmola, E.G.Vorobiev, S.M.Almo, S.C.Somasundaram, T.Chapman, M.S.Agbandje-McKenna, M.McKenna, R.

(2002) J Biol Chem 277: 20999-21006

  • DOI: 10.1074/jbc.M201371200
  • Primary Citation of Related Structures:  
    1IJJ, 1LCU

  • PubMed Abstract: 
  • An antiparallel actin dimer has been proposed to be an intermediate species during actin filament nucleation. We now show that latrunculin A, a marine natural product that inhibits actin polymerization, arrests polylysine-induced nucleation at the level of an antiparallel dimer, resulting in its accumulation ...

    An antiparallel actin dimer has been proposed to be an intermediate species during actin filament nucleation. We now show that latrunculin A, a marine natural product that inhibits actin polymerization, arrests polylysine-induced nucleation at the level of an antiparallel dimer, resulting in its accumulation. These dimers, when composed of pyrene-labeled actin subunits, give rise to a fluorescent excimer, permitting detection during polymerization in vitro. We report the crystallographic structure of the polylysine-actin-latrunculin A complex at 3.5-A resolution. The non-crystallographic contact is consistent with a dimeric structure and confirms the antiparallel orientation of its subunits. The crystallographic contacts reveal that the mobile DNase I binding loop of one subunit of a symmetry-related antiparallel actin dimer is partially stabilized in the interface between the two subunits of a second antiparallel dimer. These results provide a potential explanation for the paradoxical nucleation of actin filaments that have exclusively parallel subunits by a dimer containing antiparallel subunits.


    Related Citations: 
    • Actin-latrunculin A structure and function. Differential modulation of actin-binding protein function by latrunculin A
      Yarmola, E.G., Somasundaram, T., Boring, T.A., Spector, I., Bubb, M.R.
      (2000) J Biol Chem 275: 28120
    • Latrunculin alters the actin-monomer subunit interface to prevent polymerization
      Morton, W.M., Ayscough, K.R., McLaughlin, P.J.
      (2000) Nat Cell Biol 2: 376

    Organizational Affiliation

    Research Service, Malcom Randall Department of Veterans Affairs Medical Center and the University of Florida College of Medicine, Gainesville, Florida 32608, USA. bubbmr@medicine.ufl.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ACTIN, ALPHA SKELETAL MUSCLEA, B377Oryctolagus cuniculusMutation(s): 0 
Gene Names: ACTA1ACTA
Find proteins for P68135 (Oryctolagus cuniculus)
Explore P68135 
Go to UniProtKB:  P68135
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
LAR
Query on LAR

Download Ideal Coordinates CCD File 
E [auth A], H [auth B]LATRUNCULIN A
C22 H31 N O5 S
DDVBPZROPPMBLW-IZGXTMSKSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LARIC50:  70   nM  BindingDB
LARIC50:  40   nM  BindingDB
LARIC50:  110   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.304α = 90
b = 102.183β = 90
c = 124.218γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-04-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance