1UMR | pdb_00001umr

Crystal structure of the platelet activator convulxin, a disulfide linked a4b4 cyclic tetramer from the venom of Crotalus durissus terrificus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.264 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 

Literature

Crystal Structure of the Platelet Activator Convulxin, a Disulfide Linked A4B4 Cyclic Tetramer from the Venom of Crotalus Durissus Terrificus

Murakami, M.T., Zela, S.P., Gava, L.M., Michelan-Duarte, S., Cintra, A.C.O., Arni, R.K.

(2003) Biochem Biophys Res Commun 310: 478

  • DOI: https://doi.org/10.1016/j.bbrc.2003.09.032
  • Primary Citation Related Structures: 
    1UMR

  • PubMed Abstract: 

    Convulxin (CVX), a C-type lectin, isolated from the venom of the South American rattlesnake Crotalus durissus terrificus, causes cardiovascular and respiratory disturbances and is a potent platelet activator which binds to platelet glycoprotein GPVI. The structure of CVX has been solved at 2.4A resolution to a crystallographic residual of 18.6% (R(free)=26.4%). CVX is a disulfide linked heterodimer consisting of homologous alpha and beta chains. The heterodimers are additionally linked by disulfide bridges to form cyclic alpha(4)beta(4)heterotetramers. These domains exhibit significant homology to the carbohydrate-binding domains of C-type lectins, to the factor IX-binding protein (IX-bp), and to flavocetin-A (Fl-A) but sequence and structural differences are observed in both the domains in the putative Ca(2+)and carbohydrate binding regions.

    • Organizational Affiliation: 
    • Department of Physics, IBILCE/UNESP, R. Cristovão Colombo 2265, CEP 15054-000, São Josédo Rio Preto-SP, Brazil.

Macromolecule Content 

  • Total Structure Weight: 61.41 kDa 
  • Atom Count: 4,515 
  • Modeled Residue Count: 520 
  • Deposited Residue Count: 520 
  • Unique protein chains: 2

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CONVULXIN ALPHA
A, B
135Crotalus durissus terrificusMutation(s): 0 
UniProt
Find proteins for O93426 (Crotalus durissus terrificus)
Explore O93426 
Go to UniProtKB:  O93426
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO93426
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CONVULXIN BETA
C, D
125Crotalus durissus terrificusMutation(s): 0 
UniProt
Find proteins for O93427 (Crotalus durissus terrificus)
Explore O93427 
Go to UniProtKB:  O93427
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO93427
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.264 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.906α = 90
b = 131.906β = 90
c = 112.849γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-21
    Type: Initial release
  • Version 1.1: 2013-11-20
    Changes: Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary