4GV5

X-ray structure of crotamine, a cell-penetrating peptide from the Brazilian snake Crotalus durissus terrificus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the polypeptide crotamine from the Brazilian rattlesnake Crotalus durissus terrificus.

Coronado, M.A.Gabdulkhakov, A.Georgieva, D.Sankaran, B.Murakami, M.T.Arni, R.K.Betzel, C.

(2013) Acta Crystallogr.,Sect.D 69: 1958-1964

  • DOI: 10.1107/S0907444913018003

  • PubMed Abstract: 
  • The crystal structure of the myotoxic, cell-penetrating, basic polypeptide crotamine isolated from the venom of Crotalus durissus terrificus has been determined by single-wavelength anomalous dispersion techniques and refined at 1.7 Å resolution. The ...

    The crystal structure of the myotoxic, cell-penetrating, basic polypeptide crotamine isolated from the venom of Crotalus durissus terrificus has been determined by single-wavelength anomalous dispersion techniques and refined at 1.7 Å resolution. The structure reveals distinct cationic and hydrophobic surface regions that are located on opposite sides of the molecule. This surface-charge distribution indicates its possible mode of interaction with negatively charged phospholipids and other molecular targets to account for its diverse pharmacological activities. Although the sequence identity between crotamine and human β-defensins is low, the three-dimensional structures of these functionally related peptides are similar. Since crotamine is a leading member of a large family of myotoxic peptides, its structure will provide a basis for the design of novel cell-penetrating molecules.


    Organizational Affiliation

    Multi User Center for Biomolecular Innovation, Department of Physics, São Paulo State University, UNESP/IBILCE, C. Postal 136, 15054-000 São José do Rio Preto-SP, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Crotamine Ile-19
A, B, C
42Crotalus durissus terrificusMutation(s): 0 
Gene Names: CRO2 (CRT-P1)
Find proteins for Q9PWF3 (Crotalus durissus terrificus)
Go to UniProtKB:  Q9PWF3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SCN
Query on SCN

Download SDF File 
Download CCD File 
A, B, C
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.167 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.922α = 90.00
b = 74.330β = 90.00
c = 80.199γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
AutoSolphasing
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2013-10-23
    Type: Database references
  • Version 1.2: 2018-03-07
    Type: Data collection