1IJJ | pdb_00001ijj

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 (Depositor) 
  • R-Value Work: 
    0.233 (Depositor) 

Starting Model: experimental
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This is version 1.3 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 Biological Chem 277: 20999-21006

  • DOI: https://doi.org/10.1074/jbc.M201371200
  • Primary Citation 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. 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.

    • 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

Macromolecule Content 

  • Total Structure Weight: 86.1 kDa 
  • Atom Count: 5,674 
  • Modeled Residue Count: 734 
  • Deposited Residue Count: 754 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ACTIN, ALPHA SKELETAL MUSCLE
A, B
377Oryctolagus cuniculusMutation(s): 0 
EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus)
Explore P68135 
Go to UniProtKB:  P68135
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68135
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

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

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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
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description