PDBsum entry 1xt3

Toxin

PDB id: 1xt3

Contents

Protein chains

60 a.a. *

Ligands

SGN-IDS-SGN-IDS-SGN-IDS

CIT

Waters ×10

* Residue conservation analysis

PDB id:

1xt3

Name:

Toxin

Title:

Structure basis of venom citrate-dependent heparin sulfate-mediated cell surface retention of cobra cardiotoxin a3

Structure:

Cytotoxin 3. Chain: a, b. Synonym: cardiotoxin 3, ctx-3, cardiotoxin analog iii, ctx iii

Source:

Naja atra. Chinese cobra. Organism_taxid: 8656

Resolution:

2.40Å R-factor: 0.227 R-free: 0.250

Authors:

S.-C.Lee,H.-H.Guan,C.-H.Wang,W.-N.Huang,C.-J.Chen,W.-G.Wu

Key ref:

S.C.Lee et al. (2005). Structural basis of citrate-dependent and heparan sulfate-mediated cell surface retention of cobra cardiotoxin A3. J Biol Chem, 280, 9567-9577. PubMed id: 15590643 DOI: 10.1074/jbc.M412398200

Date:

21-Oct-04 Release date: 14-Dec-04

Protein chains

P60301  (3SA3_NAJAT) -  Cytotoxin 3 from Naja atra

Seq: 81 a.a.

Struc: 60 a.a.

DOI no: 10.1074/jbc.M412398200

J Biol Chem 280:9567-9577 (2005)

PubMed id: 15590643

Structural basis of citrate-dependent and heparan sulfate-mediated cell surface retention of cobra cardiotoxin A3.

S.C.Lee, H.H.Guan, C.H.Wang, W.N.Huang, S.C.Tjong, C.J.Chen, W.G.Wu.

ABSTRACT

Anionic citrate is a major component of venom, but the role of venom citrate in toxicity other than its inhibitory effect on the cation-dependent action of venom toxins is poorly understood. By immobilizing Chinese hamster ovary cells in microcapillary tubes and heparin on sensor chips, we demonstrated that heparan sulfate-mediated cell retention of the major cardiotoxin (CTX) from the Taiwan cobra, CTX A3, near membrane surfaces is citrate-dependent. X-ray determination of a CTX A3-heparin hexasaccharide complex structure at 2.4 A resolution revealed a molecular mechanism for toxin retention in which heparin-induced conformational changes of CTX A3 lead to citrate-mediated dimerization. A citrate ion bound to Lys-23 and Lys-31 near the tip of loop II stabilizes hydrophobic contact of the CTX A3 homodimer at the functionally important loop I and II regions. Additionally, the heparin hexasaccharide interacts with five CTX A3 molecules in the crystal structure, providing another mechanism whereby the toxin establishes a complex network of interactions that result in a strong interaction with cell surfaces presenting heparan sulfate. Our results suggest a novel role for venom citrate in biological activity and reveal a structural model that explains cell retention of cobra CTX A3 through heparan sulfate-CTX interactions.

Selected figure(s)

Figure 4.
FIG. 4. Structure of CTX A3 dimer in complex with heparin hexasaccharide at 2.4 Å resolution. A, dimeric packing of toxin with one heparin hexasaccharide bound to the positively charged cluster composed of Lys-12, Lys-18, and Lys-35 in monomer A (blue). The two CTX A3 molecules are shown in as the -carbon backbone, and the heparin hexasaccharide and citrate are shown as stick representations. B, top (1), citrate bound to Lys-31 and Lys-23 of monomer A and B with an electrostatic contact of 3-4 Å. B (bottom), 2F[o] - F[c] electron density map for the citrate ion and the charged cluster formed by Lys-31 and Lys-23 of the two monomers. C, electrostatic surface of the CTX A3 dimer showing citrate bound to a highly positively charged cluster generated by dimer formation. D, view of CTX A3 dimer showing two heparin-binding sites that are potential sites for toxin retention on heparin surfaces.

Figure 8.
FIG. 8. Representations of cis and trans binding of heparin by CTX A3 dimers and of trans complex bound to SDS. A, cis form of heparin-induced CTX A3 dimer based on asymmetry unit of CTX A3-heparin-citrate complex. CTX, heparin, and citrate are shown in blue, red, and pink, respectively. B, trans form of heparin-induced CTX A3 dimer based on crystal packing of CTX A3-heparin-citrate complex. The colors of molecules are the same as in A. C, trans form of heparin-CTX A3 dimer complex formation based on D1 dimer packing in CTX A3-SDS complex (PDB code 1H0J [PDB] ). Modeling of CTX-heparin-SDS complexes were performed on a Silicon Graphics O2 work station with Insight II 2000 (Accelrys Co., San Diego). Fully sulfated heparin hexasaccharide was adapted from a published PDB structure (PDB code 1PHN [PDB] ). Energy calculations were performed with modified Amber force field with sulfate parameter extension (42). Initial position of heparin hexasaccharide was manually docked with the evaluation of lowest intermolecular energy by Docking module of Insight II. The sulfate and carboxylate groups of hexasaccharide at reducing and nonreducing ends were located at heparin-binding pockets of CTXs. Energy minimization was then performed by Discover. CTX, heparin, and SDS are shown in blue, red, and green, respectively. The membrane interface was arbitrarily picked based on the hydrophobic region of CTX A3 surrounded by bound SDS in D1 dimer of CTX A3-SDS complex.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 9567-9577) copyright 2005.

Figures were selected by the author.