7UIE | pdb_00007uie

Crystal structure of HcE-JLE-G6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free: 
    0.273 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7UIE

This is version 1.3 of the entry. See complete history

Literature

Structural basis for botulinum neurotoxin E recognition of synaptic vesicle protein 2.

Liu, Z.Lee, P.G.Krez, N.Lam, K.H.Liu, H.Przykopanski, A.Chen, P.Yao, G.Zhang, S.Tremblay, J.M.Perry, K.Shoemaker, C.B.Rummel, A.Dong, M.Jin, R.

(2023) Nat Commun 14: 2338-2338

  • DOI: https://doi.org/10.1038/s41467-023-37860-8
  • Primary Citation Related Structures: 
    7UIA, 7UIB, 7UIE

  • PubMed Abstract: 

    Botulinum neurotoxin E (BoNT/E) is one of the major causes of human botulism and paradoxically also a promising therapeutic agent. Here we determined the co-crystal structures of the receptor-binding domain of BoNT/E (H C E) in complex with its neuronal receptor synaptic vesicle glycoprotein 2A (SV2A) and a nanobody that serves as a ganglioside surrogate. These structures reveal that the protein-protein interactions between H C E and SV2 provide the crucial location and specificity information for H C E to recognize SV2A and SV2B, but not the closely related SV2C. At the same time, H C E exploits a separated sialic acid-binding pocket to mediate recognition of an N-glycan of SV2. Structure-based mutagenesis and functional studies demonstrate that both the protein-protein and protein-glycan associations are essential for SV2A-mediated cell entry of BoNT/E and for its potent neurotoxicity. Our studies establish the structural basis to understand the receptor-specificity of BoNT/E and to engineer BoNT/E variants for new clinical applications.


  • Organizational Affiliation
    • Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, 92697, USA.

Macromolecule Content 

  • Total Structure Weight: 323.18 kDa 
  • Atom Count: 21,293 
  • Modeled Residue Count: 2,660 
  • Deposited Residue Count: 2,805 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
JLE-G6A [auth B],
C,
E,
G [auth I],
H [auth G]
138Vicugna pacosMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Botulinum neurotoxin E heavy chainB [auth A],
D,
F,
I [auth H],
J
423Clostridium botulinumMutation(s): 0 
UniProt
Find proteins for Q00496 (Clostridium botulinum)
Explore Q00496 
Go to UniProtKB:  Q00496
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00496
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free:  0.273 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.737α = 90
b = 174.626β = 90
c = 214.439γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-11-08
    Changes: Database references
  • Version 1.3: 2024-10-23
    Changes: Structure summary