4GV5 | pdb_00004gv5

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

PDB DOI: https://doi.org/10.2210/pdb4GV5/pdb

Classification: TOXIN
Organism(s): Crotalus durissus terrificus
Mutation(s): No

Deposited: 2012-08-30 Released: 2013-09-04
Deposition Author(s): Coronado, M.A., Gabdulkhakov, A., Georgieva, D., Sankaran, B., Murakami, M.T., Arni, R.K., Betzel, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.225 (Depositor), 0.224 (DCC)
R-Value Work:
0.167 (Depositor), 0.172 (DCC)
R-Value Observed:
0.170 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 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 D Biol Crystallogr 69: 1958-1964

PubMed: 24100315 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S0907444913018003
Primary Citation Related Structures:
4GV5

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 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.

Macromolecule Content

Total Structure Weight: 15.6 kDa
Atom Count: 1,136
Modeled Residue Count: 126
Deposited Residue Count: 126
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Crotamine Ile-19	A, B, C	42	Crotalus durissus terrificus	Mutation(s): 0
UniProt
Find proteins for Q9PWF3 (Crotalus durissus terrificus) Explore Q9PWF3 Go to UniProtKB: Q9PWF3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9PWF3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C]	H [auth B], I [auth B], K [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Interactions & Density Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain M [auth C] SDF format, chain N [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C]	F [auth A], G [auth A], M [auth C], N [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth C] Focus chain N [auth C]
SCN Query on SCN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C]	D [auth A], E [auth A], J [auth B], L [auth C]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.225 (Depositor), 0.224 (DCC)
R-Value Work: 0.167 (Depositor), 0.172 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.922	α = 90
b = 74.33	β = 90
c = 80.199	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AutoSol	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-09-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-09-04
Type: Initial release
Version 1.1: 2013-10-23
Changes: Database references
Version 1.2: 2018-03-07
Changes: Data collection
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-11-20
Changes: Structure summary