1QZ5

Structure of rabbit actin in complex with kabiramide C

• PDB DOI:  https://doi.org/10.2210/pdb1QZ5/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Oryctolagus cuniculus
• Mutation(s): Yes 


• Deposited: 2003-09-15 Released: 2003-11-11 
• Deposition Author(s): Klenchin, V.A., Allingham, J.S., King, R., Tanaka, J., Marriott, G., Rayment, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.187 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 

Literature

Trisoxazole macrolide toxins mimic the binding of actin-capping proteins to actin

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

(2003) Nat Struct Biol 10: 1058-1063

• PubMed: 14578936 
• DOI: https://doi.org/10.1038/nsb1006
• Primary Citation of Related Structures:  
  1QZ5, 1QZ6


• PubMed Abstract: 
  

Marine macrolide toxins of trisoxazole family target actin with high affinity and specificity and have promising pharmacological properties. We present X-ray structures of actin in complex with two members of this family, kabiramide C and jaspisamide A, at a resolution of 1.45 and 1.6 A, respectively. The structures reveal the absolute stereochemistry of these toxins and demonstrate that their trisoxazole ring interacts with actin subdomain 1 while the aliphatic side chain is inserted into the hydrophobic cavity between actin subdomains 1 and 3. The binding site is essentially the same as the one occupied by the actin-capping domain of the gelsolin superfamily of proteins. The structural evidence suggests that actin filament severing and capping by these toxins is also analogous to that of gelsolin. Consequently, these macrolides may be viewed as small molecule biomimetics of an entire class of actin-binding proteins.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.37 kDa 
• Atom Count: 3,299 
• Modelled Residue Count: 359 
• Deposited Residue Count: 375 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A	375	Oryctolagus cuniculus	Mutation(s): 1  Gene Names: ACTA1, ACTA
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135  Go to UniProtKB:  P68135

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KAB	D [auth A]	KABIRAMIDE C C48 H75 N5 O14 XYKNXOJYKRVXBX-ZAUPHERQSA-N
ATP	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC	A	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.187 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.919	α = 90
b = 70.617	β = 90
c = 75.13	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-11 
Deposition Author(s): Klenchin, V.A., Allingham, J.S., King, R., Tanaka, J., Marriott, G., Rayment, I.

Revision History  

• Version 1.0: 2003-11-11
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance