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 22QT | pdb_000022qt

Cryo-EM structure of the Deg-3/Des-2 betaine-bound intermediate state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 22QT

This is version 1.1 of the entry. See complete history. 

Literature

Structural basis of ligand recognition and gating in a heteromeric Deg-3/Des-2 nicotinic acetylcholine receptor.

Ning, Y., Jiang, Q., Lu, Z., Yu, J., Ge, J.

(2026) Proc Natl Acad Sci U S A 123: e2608998123-e2608998123

  • DOI: https://doi.org/10.1073/pnas.2608998123
  • Primary Citation Related Structures: 
    22QS, 22QT, 22QU, 22QV, 22QW

  • PubMed Abstract: 

    During evolution, nicotinic acetylcholine receptors (nAChRs) have diversified in subunit composition and ligand selectivity, enabling a conserved ion channel scaffold to support a broad range of signaling functions beyond classical synaptic transmission. Deg-3/Des-2 is a nematode-specific, calcium-permeable heteromeric α-type nicotinic receptor in sensory neurons to mediate chemosensation, nociception, and mechanotransduction, and represents a promising anthelmintic target. Here, we report cryo-electron microscopy structures of Deg-3/Des-2 in its apo, agonist-bound intermediate and agonist-bound open states. Deg-3/Des-2 adopts a 2Deg-3:3Des-2 stoichiometry. Five agonist molecules occupy intersubunit orthosteric sites, driving channel opening primarily through rotational rearrangements of the upper M2 helices that relieve a conserved hydrophobic gate and enable calcium permeation. We further identify a Deg-3-specific N-terminal helix that regulates desensitization and a negatively charged extracellular vestibular helix that governs calcium permeability. Together, these structures reveal how evolutionary tuning of ligand recognition, ion selectivity, and gating within a conserved nicotinic receptor framework.


  • Organizational Affiliation: 
    • School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.

Macromolecule Content 

  • Total Structure Weight: 321.87 kDa 
  • Atom Count: 16,110 
  • Modeled Residue Count: 1,924 
  • Deposited Residue Count: 2,772 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetylcholine receptor subunit alpha-type des-2A,
C [auth B],
E [auth C]
548Caenorhabditis elegansMutation(s): 0 
Gene Names: des-2, acr-4, T26H10.1
UniProt
Find proteins for O76554 (Caenorhabditis elegans)
Explore O76554 
Go to UniProtKB:  O76554
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76554
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetylcholine receptor subunit alpha-type deg-3B [auth D],
D [auth E]
564Caenorhabditis elegansMutation(s): 0 
Gene Names: deg-3, K03B8.9
UniProt
Find proteins for P54244 (Caenorhabditis elegans)
Explore P54244 
Go to UniProtKB:  P54244
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54244
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, M
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, I, J, K
G, H, I, J, K, L
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

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

Query on NAG



Download:Ideal Coordinates CCD File
O [auth A],
P [auth A],
S [auth B],
V [auth C],
W [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
BET
(Subject of Investigation/LOI)

Query on BET



Download:Ideal Coordinates CCD File
N [auth A],
Q [auth D],
R [auth B],
T [auth E],
U [auth C]
TRIMETHYL GLYCINE
C5 H12 N O2
KWIUHFFTVRNATP-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-12
    Type: Initial release
  • Version 1.1: 2026-10-07
    Changes: Data collection, Database references