Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.71 kDa 
• Atom Count: 1209 
• Residue Count: 144 
• Unique protein chains: 1

1XA5

Structure of Calmodulin in complex with KAR-2, a bis-indol alkaloid

• DOI: 10.2210/pdb1XA5/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2004-08-25 Released: 2004-12-21 
• Deposition Author(s): Horvath, I., Harmat, V., Hlavanda, E., Naray-Szabo, G., Ovadi, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.261 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

Literature

The structure of the complex of calmodulin with KAR-2: a novel mode of binding explains the unique pharmacology of the drug

Horvath, I., Harmat, V., Perczel, A., Palfi, V., Nyitrai, L., Nagy, A., Hlavanda, E., Naray-Szabo, G., Ovadi, J.

(2005) J Biol Chem 280: 8266-8274

• PubMed: 15596444 
• DOI: 10.1074/jbc.M410353200
• Primary Citation of Related Structures:  
  1XA5


• PubMed Abstract: 
  

3'-(beta-Chloroethyl)-2',4'-dioxo-3,5'-spiro-oxazolidino-4-deacetoxyvinblastine (KAR-2) is a potent anti-microtubular agent that arrests mitosis in cancer cells without significant toxic side effects. In this study we demonstrate that in addition to targeting microtubules, KAR-2 also binds calmodulin, thereby countering the antagonistic effects of trifluoperazine. To determine the basis of both properties of KAR-2, the three-dimensional structure of its complex with Ca(2+)-calmodulin has been characterized both in solution using NMR and when crystallized using x-ray diffraction. Heterocorrelation ((1)H-(15)N heteronuclear single quantum coherence) spectra of (15)N-labeled calmodulin indicate a global conformation change (closure) of the protein upon its binding to KAR-2. The crystal structure at 2.12-A resolution reveals a more complete picture; KAR-2 binds to a novel structure created by amino acid residues of both the N- and C-terminal domains of calmodulin. Although first detected by x-ray diffraction of the crystallized ternary complex, this conformational change is consistent with its solution structure as characterized by NMR spectroscopy. It is noteworthy that a similar tertiary complex forms when calmodulin binds KAR-2 as when it binds trifluoperazine, even though the two ligands contact (for the most part) different amino acid residues. These observations explain the specificity of KAR-2 as an anti-microtubular agent; the drug interacts with a novel drug binding domain on calmodulin. Consequently, KAR-2 does not prevent calmodulin from binding most of its physiological targets.

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Organizational Affiliation: 

Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Karolina út 29 Budapest, H-1113 Hungary.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin	A	148	Bos taurus	Mutation(s): 0  Gene Names: CALM, CAM
Find proteins for P62157 (Bos taurus) Explore P62157  Go to UniProtKB:  P62157

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KAR	A	3"-(BETA-CHLOROETHYL)-2",4"-DIOXO-3, 5"-SPIRO-OXAZOLIDINO-4-DEACETOXY-VINBLASTINE C46 H56 Cl N5 O7 NUXKIZBEPYVRKP-RWBWKAGLSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
KAR	Kd :  316   nM  PDBBind
KAR	Kd:  316   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.261 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.573	α = 90
b = 37.573	β = 90
c = 356.662	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-08-25 
• Released Date: 2004-12-21 
Deposition Author(s): Horvath, I., Harmat, V., Hlavanda, E., Naray-Szabo, G., Ovadi, J.

Revision History 

• Version 1.0: 2004-12-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2018-10-03
  Changes: Data collection