1XT3

Structure Basis of Venom Citrate-Dependent Heparin Sulfate-Mediated Cell Surface Retention of Cobra Cardiotoxin A3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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

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

(2005) J.Biol.Chem. 280: 9567-9577

  • DOI: 10.1074/jbc.M412398200

  • PubMed 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 microcapilla ...

    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.


    Organizational Affiliation

    Institute of Bioinformatics and Structural Biology, National TsingHua University, Hsinchu 30043, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytotoxin 3
A, B
60Naja atraMutation(s): 0 
Find proteins for P60301 (Naja atra)
Go to UniProtKB:  P60301
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
SGN
Query on SGN

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Download CCD File 
A
N,O6-DISULFO-GLUCOSAMINE
C6 H13 N O11 S2
DQTRACMFIGDHSN-UKFBFLRUSA-N
 Ligand Interaction
IDS
Query on IDS

Download SDF File 
Download CCD File 
A
2-O-sulfo-alpha-L-idopyranuronic acid
O2-SULFO-GLUCURONIC ACID
C6 H10 O10 S
COJBCAMFZDFGFK-VCSGLWQLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.227 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 43.903α = 90.00
b = 59.447β = 90.00
c = 98.620γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description