1YXQ

Crystal structure of actin in complex with swinholide A

PDB DOI: https://doi.org/10.2210/pdb1YXQ/pdb

Classification: CONTRACTILE PROTEIN
Organism(s): Oryctolagus cuniculus
Mutation(s): Yes

Deposited: 2005-02-22 Released: 2005-05-17
Deposition Author(s): Klenchin, V.A., King, R., Tanaka, J., Marriott, G., Rayment, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.219 (Depositor), 0.220 (DCC)
R-Value Work:
0.184 (Depositor), 0.200 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural basis of swinholide a binding to actin

Klenchin, V.A., King, R., Tanaka, J., Marriott, G., Rayment, I.

(2005) Chem Biol 12: 287-291

PubMed: 15797212 Search on PubMed
DOI: https://doi.org/10.1016/j.chembiol.2005.02.011
Primary Citation of Related Structures:
1YXQ

PubMed Abstract:
Marine toxins targeting the actin cytoskeleton represent a new and promising class of anti-cancer compounds. Here we present a 2.0 A resolution structure of swinholide A, a marine macrolide, bound to two actin molecules. The structure demonstrates that the actin dimer in the complex does not represent a physiologically relevant entity, for the two actin molecules do not interact with each other. The swinholide A actin binding site is the same as that targeted by toxins of the trisoxazole family and numerous actin binding proteins, highlighting the importance of this site in actin polymerization. The observed structure reveals the mechanism of action of swinholide A and provides a structural framework about which to design new agents directed at the cytoskeleton.

Organizational Affiliation

Department of Biochemistry, University of Wisconsin at Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA.

Macromolecule Content

Total Structure Weight: 86.35 kDa
Atom Count: 6,057
Modelled Residue Count: 715
Deposited Residue Count: 750
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
actin, alpha skeletal muscle	A, B	375	Oryctolagus cuniculus	Mutation(s): 1 EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135 Go to UniProtKB: P68135
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68135
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SWI Query on SWI Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	SWINHOLIDE A C₇₈ H₁₃₂ O₂₀ RJVBVECTCMRNFG-ITCKPGCBSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	C [auth A], D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B]