7Z14 | pdb_00007z14

Cryo-EM structure of Torpedo nicotinic acetylcholine receptor in complex with a short-chain neurotoxin.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7Z14

This is version 1.2 of the entry. See complete history

Literature

The molecular mechanism of snake short-chain alpha-neurotoxin binding to muscle-type nicotinic acetylcholine receptors.

Nys, M.Zarkadas, E.Brams, M.Mehregan, A.Kambara, K.Kool, J.Casewell, N.R.Bertrand, D.Baenziger, J.E.Nury, H.Ulens, C.

(2022) Nat Commun 13: 4543-4543

  • DOI: https://doi.org/10.1038/s41467-022-32174-7
  • Primary Citation Related Structures: 
    7Z14

  • PubMed Abstract: 

    Bites by elapid snakes (e.g. cobras) can result in life-threatening paralysis caused by venom neurotoxins blocking neuromuscular nicotinic acetylcholine receptors. Here, we determine the cryo-EM structure of the muscle-type Torpedo receptor in complex with ScNtx, a recombinant short-chain α-neurotoxin. ScNtx is pinched between loop C on the principal subunit and a unique hairpin in loop F on the complementary subunit, thereby blocking access to the neurotransmitter binding site. ScNtx adopts a binding mode that is tilted toward the complementary subunit, forming a wider network of interactions than those seen in the long-chain α-Bungarotoxin complex. Certain mutations in ScNtx at the toxin-receptor interface eliminate inhibition of neuronal α7 nAChRs, but not of human muscle-type receptors. These observations explain why ScNtx binds more tightly to muscle-type receptors than neuronal receptors. Together, these data offer a framework for understanding subtype-specific actions of short-chain α-neurotoxins and inspire strategies for design of new snake antivenoms.


  • Organizational Affiliation
    • Laboratory of Structural Neurobiology, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, 3000, Leuven, Belgium. mieke.nys@kuleuven.be.

Macromolecule Content 

  • Total Structure Weight: 286.87 kDa 
  • Atom Count: 15,856 
  • Modeled Residue Count: 1,913 
  • Deposited Residue Count: 2,453 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetylcholine receptor subunit alpha
A, D
437Tetronarce californicaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P02710 (Tetronarce californica)
Explore P02710 
Go to UniProtKB:  P02710
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02710
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetylcholine receptor subunit beta469Tetronarce californicaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P02712 (Tetronarce californica)
Explore P02712 
Go to UniProtKB:  P02712
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02712
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetylcholine receptor subunit delta501Tetronarce californicaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P02718 (Tetronarce californica)
Explore P02718 
Go to UniProtKB:  P02718
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02718
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetylcholine receptor subunit gamma489Tetronarce californicaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P02714 (Tetronarce californica)
Explore P02714 
Go to UniProtKB:  P02714
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02714
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Consensus short-chain short-chain alpha-neurotoxin ScNtx
F, G
60synthetic constructMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H, K
9N-Glycosylation
Glycosylation Resources
GlyTouCan: G83161QT
GlyCosmos: G83161QT
GlyGen: G83161QT
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I, J
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
L
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G08466KH
GlyCosmos: G08466KH
GlyGen: G08466KH

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
M [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)Belgium12X2722N
KU LeuvenBelgiumC32/16/035
Wellcome TrustUnited Kingdom221710/Z/20/Z
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INSB-05-02
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)FranceANR- 17-EURE-0003
European Research Council (ERC)European Union637733 Pentabrain

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-17
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Source and taxonomy
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary