4ISQ | pdb_00004isq

Binding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.220 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4ISQ

This is version 1.3 of the entry. See complete history

Literature

Crystal Structures of Botulinum Neurotoxin DC in Complex with Its Protein Receptors Synaptotagmin I and II.

Berntsson, R.P.Peng, L.Svensson, L.M.Dong, M.Stenmark, P.

(2013) Structure 21: 1602-1611

  • DOI: https://doi.org/10.1016/j.str.2013.06.026
  • Primary Citation Related Structures: 
    4ISQ, 4ISR

  • PubMed Abstract: 

    Botulinum neurotoxins (BoNTs) can cause paralysis at exceptionally low concentrations and include seven serotypes (BoNT/A-G). The chimeric BoNT/DC toxin has a receptor binding domain similar to the same region in BoNT/C. However, BoNT/DC does not share protein receptor with BoNT/C. Instead, it shares synaptotagmin (Syt) I and II as receptors with BoNT/B, despite their low sequence similarity. Here, we present the crystal structures of the binding domain of BoNT/DC in complex with the recognition domains of its protein receptors, Syt-I and Syt-II. The structures reveal that BoNT/DC possesses a Syt binding site, distinct from the established Syt-II binding site in BoNT/B. Structure-based mutagenesis further shows that hydrophobic interactions play a key role in Syt binding. The structures suggest that the BoNT/DC ganglioside binding sites are independent of the protein receptor binding site. Our results reveal the remarkable versatility in the receptor recognition of the BoNTs.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden.

Macromolecule Content 

  • Total Structure Weight: 160.27 kDa 
  • Atom Count: 10,970 
  • Modeled Residue Count: 1,286 
  • Deposited Residue Count: 1,356 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neurotoxin
A, B, C
431Clostridium botulinumMutation(s): 0 
UniProt
Find proteins for Q9LBR1 (Clostridium botulinum)
Explore Q9LBR1 
Go to UniProtKB:  Q9LBR1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LBR1
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Synaptotagmin-1
D, E, F
21Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P21579 (Homo sapiens)
Explore P21579 
Go to UniProtKB:  P21579
PHAROS:  P21579
GTEx:  ENSG00000067715 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21579
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
X [auth C],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
FA [auth C]
GA [auth C]
HA [auth C]
M [auth A]
N [auth A]
FA [auth C],
GA [auth C],
HA [auth C],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
W [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.220 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.227α = 90
b = 57.55β = 118.11
c = 165.274γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Database references
  • Version 1.2: 2018-04-18
    Changes: Data collection
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations