1KOZ | pdb_00001koz

SOLUTION STRUCTURE OF OMEGA-GRAMMOTOXIN SIA


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Solution structure of omega-grammotoxin SIA, a gating modifier of P/Q and N-type Ca(2+) channel.

Takeuchi, K.Park, E.Lee, C.Kim, J.Takahashi, H.Swartz, K.Shimada, I.

(2002) J Mol Biology 321: 517-526

  • DOI: https://doi.org/10.1016/s0022-2836(02)00595-8
  • Primary Citation Related Structures: 
    1KOZ

  • PubMed Abstract: 

    omega-Grammotoxin SIA (GrTx) is a 36 amino acid residue protein toxin from spider venom that inhibits P/Q and N-type voltage-gated Ca(2+) channels by modifying voltage-dependent gating. We determined the three-dimensional structure of GrTx using NMR spectroscopy. The toxin adopts an "inhibitor cystine knot" motif composed of two beta-strands (Leu19-Cys21 and Cys30-Trp32) and a beta-bulge (Trp6, Gly7-Cys30) with a +2x, -1 topology, which are connected by four chain reversals. Although GrTx was originally identified as an inhibitor of voltage-gated Ca(2+) channel, it also binds to K(+) channels with lower affinity. A similar cross-reaction was observed for Hanatoxin1 (HaTx), which binds to the voltage-sensing domains of K(+) and Ca(2+) channels with different affinities. A detailed comparison of the GrTx and HaTx structures identifies a conserved face containing a large hydrophobic patch surrounded by positively charged residues. The slight differences in the surface shape, which result from the orientation of the surface aromatic residues and/or the distribution of the charged residues, may explain the differences in the binding affinity of these gating modifiers with different voltage-gated ion channels.


  • Organizational Affiliation
    • Graduate School of Pharmaceutical Sciences, The University of Tokyo, 113-0033, Tokyo, Japan.

Macromolecule Content 

  • Total Structure Weight: 4.12 kDa 
  • Atom Count: 285 
  • Modeled Residue Count: 36 
  • Deposited Residue Count: 36 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Voltage-dependent Channel Inhibitor36N/AMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P60590 (Grammostola rosea)
Explore P60590 
Go to UniProtKB:  P60590
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60590
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-08-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-10-16
    Changes: Data collection, Structure summary