2ASP

Structure of Rabbit Actin In Complex With Reidispongiolide C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of microfilament destabilizing toxins bound to actin provide insight into toxin design and activity

Allingham, J.S.Zampella, A.D'Auria, M.V.Rayment, I.

(2005) Proc.Natl.Acad.Sci.Usa 102: 14527-14532

  • DOI: 10.1073/pnas.0502089102
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Marine macrolides that disrupt the actin cytoskeleton are promising candidates for cancer treatment. Here, we present the actin-bound x-ray crystal structures of reidispongiolide A and C and sphinxolide B, three marine macrolides found among a recent ...

    Marine macrolides that disrupt the actin cytoskeleton are promising candidates for cancer treatment. Here, we present the actin-bound x-ray crystal structures of reidispongiolide A and C and sphinxolide B, three marine macrolides found among a recently discovered family of cytotoxic compounds. Their structures allow unequivocal assignment of the absolute configuration for each compound. A comparison of their actin-binding site to macrolides found in the trisoxazole family, as well as the divalent macrolide, swinholide A, reveals the existence of a common binding surface for a defined segment of their macrocyclic ring. This surface is located on a hydrophobic patch adjacent to the cleft separating domains 1 and 3 at the barbed-end of actin. The large area surrounding this surface accommodates a wide variety of conformations and designs observed in the macrocyclic component of barbed-end-targeting macrolides. Conversely, the binding pocket for the macrolide tail, located within the cleft itself, shows very limited variation. Functional characterization of these macrolides by using in vitro actin filament severing and polymerization assays demonstrate the necessity of the N-methyl-vinylformamide moiety at the terminus of the macrolide tail for toxin potency. These analyses also show the importance of stable interactions between the macrocyclic ring and the hydrophobic patch on actin for modifying filament structure and how this stability can be compromised by subtle changes in macrolactone ring composition. By identifying the essential components of these complex natural products that underlie their high actin affinity, we have established a framework for designing new therapeutic agents.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin, Madison, WI 53706-1544, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Actin, alpha skeletal muscle
A
375Oryctolagus cuniculusMutation(s): 0 
Gene Names: ACTA1 (ACTA)
Find proteins for P68135 (Oryctolagus cuniculus)
Go to Gene View: ACTA1
Go to UniProtKB:  P68135
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
RGC
Query on RGC

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A
REIDISPONGIOLIDE C
(4R,5R,9S,10S,11S)-4,10-DIMETHOXY-5,9-DIMETHYL-6-OXO-11-((3R,5Z,7Z,11S,12S,13Z,15R,17S,18S,19Z,21S,23S,24R,25R)-3,15,17,21,23-PENTAMETHOXY-5,12,18,24-TETRAMETHYL-9,27-DIOXO-10,26-DIOXABICYCLO[23.3.1]NONACOSA-1(28),5,7,13,19-PENTAEN-11-YL)DODECANOIC ACID
C52 H84 O14
QTLSHCJDXCYLJK-VRWAWWQJSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.163 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 170.402α = 90.00
b = 54.689β = 95.81
c = 40.872γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance