1WUA

The structure of Aplyronine A-actin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

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This is version 1.3 of the entry. See complete history


Literature

Structure basis for antitumor effect of aplyronine a

Hirata, K.Muraoka, S.Suenaga, K.Kuroda, T.Kato, K.Tanaka, H.Yamamoto, M.Takata, M.Yamada, K.Kigoshi, H.

(2006) J Mol Biol 356: 945-954

  • DOI: https://doi.org/10.1016/j.jmb.2005.12.031
  • Primary Citation of Related Structures:  
    1WUA

  • PubMed Abstract: 

    Aplyronine A, isolated from the sea hare Aplysia kurodai, possesses an exceedingly potent antitumor effect in vivo and it is one of the promising candidates as an anticancer drug. This macrolide is known to depolymerize F-actin and inhibit the polymerization of actin by forming a 1:1 complex with monomeric actin. The first complex structure of actin-aplyronine A was determined via a synchrotron X-ray analysis at a 1.45 A resolution. As expected, aplyronine A binds to a hydrophobic cleft composed of subdomains 1 and 3 of actin by intercalating its aliphatic tail part into the actin molecule as do the other reported F-actin depolymerizing agents. Unexpectedly, this complex structure shows the specific structural features around the trimethylserine moiety, revealed as an important moiety of aplyronine A for cytotoxicity against HeLa cells. Combining this result and our previous one, the moiety should strongly relate to the specific biological activity of aplyronine A; i.e. a potent antitumor effect.


  • Organizational Affiliation

    JASRI/SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5198 Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, alpha skeletal muscle375Oryctolagus cuniculusMutation(s): 1 
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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AP8
Query on AP8

Download Ideal Coordinates CCD File 
D [auth A](8R,9R,10R,11R,14S,18S,20S,24S)-24-{(1R,2S,3R,6R,7R,8R,9S,10E)-8-(ACETYLOXY)-6-[(N,N-DIMETHYLALANYL)OXY]-11-[FORMYL(MET HYL)AMINO]-2-HYDROXY-1,3,7,9-TETRAMETHYLUNDEC-10-ENYL}-10-HYDROXY-14,20-DIMETHOXY-9,11,15,18-TETRAMETHYL-2-OXOOXACYCLOTE TRACOSA-3,5,15,21-TETRAEN-8-YL N,N,O-TRIMETHYLSERINATE
C59 H101 N3 O14
JMXMEKJLQWJRHY-GDEZZODWSA-N
ATP
Query on ATP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
A
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.704α = 90
b = 75.123β = 95.23
c = 67.546γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary