4QD2 | pdb_00004qd2

Molecular basis for disruption of E-cadherin adhesion by botulinum neurotoxin A complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.247 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history. 

Literature

Molecular basis for disruption of E-cadherin adhesion by botulinum neurotoxin A complex.

Lee, K., Zhong, X., Gu, S., Kruel, A.M., Dorner, M.B., Perry, K., Rummel, A., Dong, M., Jin, R.

(2014) Science 344: 1405-1410

  • DOI: https://doi.org/10.1126/science.1253823
  • Primary Citation Related Structures: 
    4QD2

  • PubMed Abstract: 

    How botulinum neurotoxins (BoNTs) cross the host intestinal epithelial barrier in foodborne botulism is poorly understood. Here, we present the crystal structure of a clostridial hemagglutinin (HA) complex of serotype BoNT/A bound to the cell adhesion protein E-cadherin at 2.4 angstroms. The HA complex recognizes E-cadherin with high specificity involving extensive intermolecular interactions and also binds to carbohydrates on the cell surface. Binding of the HA complex sequesters E-cadherin in the monomeric state, compromising the E-cadherin-mediated intercellular barrier and facilitating paracellular absorption of BoNT/A. We reconstituted the complete 14-subunit BoNT/A complex using recombinantly produced components and demonstrated that abolishing either E-cadherin- or carbohydrate-binding of the HA complex drastically reduces oral toxicity of BoNT/A complex in vivo. Together, these studies establish the molecular mechanism of how HAs contribute to the oral toxicity of BoNT/A.

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

Macromolecule Content 

  • Total Structure Weight: 274.92 kDa 
  • Atom Count: 19,012 
  • Modeled Residue Count: 2,303 
  • Deposited Residue Count: 2,412 
  • Unique protein chains: 4

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin component HA33A [auth D],
C,
F [auth I],
H		296Clostridium botulinum A str. HallMutation(s): 0 
Gene Names: ha70, CBO0801, CLC_0857
UniProt
Find proteins for A5HZZ6 (Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A))
Explore A5HZZ6 
Go to UniProtKB:  A5HZZ6
Entity Groups
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UniProt GroupA5HZZ6
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin component HA17
B, G
147Clostridium botulinum A str. HallMutation(s): 0 
Gene Names: ha17, CBO0802, CLC_0858
UniProt
Find proteins for A5HZZ5 (Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A))
Explore A5HZZ5 
Go to UniProtKB:  A5HZZ5
Entity Groups
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UniProt GroupA5HZZ5
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Reference Sequence
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|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin component HA70D [auth A],
I [auth F]		254Clostridium botulinum A str. HallMutation(s): 0 
Gene Names: ha33, CBO0803, CLC_0859
UniProt
Find proteins for A5HZZ4 (Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A))
Explore A5HZZ4 
Go to UniProtKB:  A5HZZ4
Entity Groups
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UniProt GroupA5HZZ4
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Reference Sequence
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|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Cadherin-1
E, J
213Mus musculusMutation(s): 0 
Gene Names: Cdh1
UniProt & NIH Common Fund Data Resources
Find proteins for P09803 (Mus musculus)
Explore P09803 
Go to UniProtKB:  P09803
IMPC:  MGI:88354
Entity Groups
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UniProt GroupP09803
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.247 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.99α = 116.89
b = 95.73β = 96.34
c = 96.14γ = 93.7
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2014-07-02
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description