1VB0 | pdb_00001vb0

Atomic resolution structure of atratoxin-b, one short-chain neurotoxin from Naja atra

• PDB DOI: https://doi.org/10.2210/pdb1VB0/pdb

• Classification: TOXIN
• Organism(s): Naja atra
• Mutation(s): No 


• Deposited: 2004-02-20 Released: 2004-12-21 
• Deposition Author(s): Lou, X., Liu, Q., Teng, M., Niu, L., Huang, Q., Hao, Q.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.92 Å
• R-Value Free: 
  0.133 (Depositor) 
• R-Value Work: 
  0.114 (Depositor) 

Starting Model: experimental

Literature

The atomic resolution crystal structure of atratoxin determined by single wavelength anomalous diffraction phasing

Lou, X., Liu, Q., Tu, X., Wang, J., Teng, M., Niu, L., Schuller, D.J., Huang, Q., Hao, Q.

(2004) J Biological Chem 279: 39094-39104

• PubMed: 15252034 
• DOI: https://doi.org/10.1074/jbc.M403863200
• Primary Citation Related Structures: 
  1V6P, 1VB0


• PubMed Abstract: 
  

  By using single wavelength anomalous diffraction phasing based on the anomalous signal from copper atoms, the crystal structure of atratoxin was determined at the resolution of 1.5 A and was refined to an ultrahigh resolution of 0.87 A. The ultrahigh resolution electron density maps allowed the modeling of 38 amino acid residues in alternate conformations and the location of 322 of 870 possible hydrogen atoms. To get accurate information at the atomic level, atratoxin-b (an analog of atratoxin with reduced toxicity) was also refined to an atomic resolution of 0.92 A. By the sequence and structural comparison of these two atratoxins, Arg(33) and Arg(36) were identified to be critical to their varied toxicity. The effect of copper ions on the distribution of hydrogen atoms in atratoxin was discussed, and the interactions between copper ions and protein residues were analyzed based on a statistical method, revealing a novel pentahedral copper-binding motif.

---

Organizational Affiliation: 
• Key Laboratory of Structural Biology, Chinese Academy of Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.06 kDa 
• Atom Count: 652 
• Modeled Residue Count: 61 
• Deposited Residue Count: 61 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobrotoxin b	A	61	Naja atra	Mutation(s): 0
UniProt
Find proteins for P80958 (Naja atra) Explore P80958  Go to UniProtKB:  P80958

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.92 Å
• R-Value Free:  0.133 (Depositor) 
• R-Value Work:  0.114 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.463	α = 90
b = 48.463	β = 90
c = 44.133	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	model building
SHELXL-97	refinement
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-21 
Deposition Author(s): Lou, X., Liu, Q., Teng, M., Niu, L., Huang, Q., Hao, Q.

Revision History  

• Version 1.0: 2004-12-21
  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: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary