22QW | pdb_000022qw

Cryo-EM structure of the Deg-3/Des-2 choline-bound open state

PDB DOI: https://doi.org/10.2210/pdb22QW/pdb
EM Map EMD-68611: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Caenorhabditis elegans
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2026-01-21 Released: 2026-08-12
Deposition Author(s): Ning, Y., Ge, J., Yu, J.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.77 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

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This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of the Deg-3/Des-2 apo state

Ning, Y., Ge, J., Yu, J.

To be published.

Macromolecule Content

Total Structure Weight: 321.8 kDa
Atom Count: 16,091
Modeled Residue Count: 1,924
Deposited Residue Count: 2,772
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholine receptor subunit alpha-type des-2	A, C [auth B], E [auth C]	548	Caenorhabditis elegans	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O76554
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain C [auth B] Focus chain E [auth C]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholine receptor subunit alpha-type deg-3	B [auth D], D [auth E]	564	Caenorhabditis elegans	Mutation(s): 0 Gene Names: deg-3, K03B8.9
UniProt
Find proteins for P54244 (Caenorhabditis elegans) Explore P54244 Go to UniProtKB: P54244
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54244
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B [auth D] Focus chain D [auth E]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, M	3		N-Glycosylation	Interactions Focus chain F Focus chain M Interactions & Density Focus chain F Focus chain M

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	2		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain T [auth B] SDF format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain T [auth B] MOL2 format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain T [auth B] mmCIF format, chain O [auth A]	O [auth A], P [auth A], T [auth B], V [auth C], W [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Focus chain T [auth B] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain O [auth A] Focus chain P [auth A] Focus chain T [auth B] Focus chain V [auth C] Focus chain W [auth C]
CHT( Subject of Investigation/LOI) Query on CHT Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain U [auth C] SDF format, chain R [auth D] SDF format, chain Q [auth A] SDF format, chain N [auth A] MOL2 format, chain S [auth B] MOL2 format, chain U [auth C] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain N [auth A] mmCIF format, chain S [auth B] mmCIF format, chain U [auth C] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain N [auth A]	N [auth A], Q [auth A], R [auth D], S [auth B], U [auth C]	CHOLINE ION C₅ H₁₄ N O OEYIOHPDSNJKLS-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain Q [auth A] Focus chain R [auth D] Focus chain S [auth B] Focus chain U [auth C] Interactions & Density Focus chain N [auth A] Focus chain Q [auth A] Focus chain R [auth D] Focus chain S [auth B] Focus chain U [auth C]