8YQN | pdb_00008yqn

Torpedo acetylcholine receptor in complex with Erabutoxin A

PDB DOI: https://doi.org/10.2210/pdb8YQN/pdb
EM Map EMD-39500: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Tetronarce californica, Laticauda semifasciata
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes MemProtMD

Deposited: 2024-03-19 Released: 2025-05-28
Deposition Author(s): Chan, C.Y.L., Li, H.H., Hibbs, R.E., Kini, R.M.
Funding Organization(s): Ministry of Education (MoE, Singapore)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structure of Erabutoxin bound to Torpedo acetylcholine receptor gives insight to intramolecular selectivity

Chan, C.Y.L., Li, H.H., Hibbs, R.E., Kini, R.M.

To be published.

Macromolecule Content

Total Structure Weight: 291.06 kDa
Atom Count: 18,056
Modeled Residue Count: 2,166
Deposited Residue Count: 2,457
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholine receptor subunit alpha	A, D	437	Tetronarce californica	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P02710 (Tetronarce californica) Explore P02710 Go to UniProtKB: P02710
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02710
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain D
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholine receptor subunit delta	B	501	Tetronarce californica	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P02718 (Tetronarce californica) Explore P02718 Go to UniProtKB: P02718
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02718
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholine receptor subunit beta	C	469	Tetronarce californica	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P02712 (Tetronarce californica) Explore P02712 Go to UniProtKB: P02712
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02712
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholine receptor subunit gamma	E	489	Tetronarce californica	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P02714 (Tetronarce californica) Explore P02714 Go to UniProtKB: P02714
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02714
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain E
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Erabutoxin a	F, G	62	Laticauda semifasciata	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P60775 (Laticauda semifasciata) Explore P60775 Go to UniProtKB: P60775
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60775
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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, I	9		N-Glycosylation	Interactions Focus chain H Focus chain I Interactions & Density Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G83161QT GlyCosmos: G83161QT GlyGen: G83161QT

Entity ID: 7
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	J, K	3		N-Glycosylation	Interactions Focus chain J Focus chain K Interactions & Density Focus chain J Focus chain K
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	5		N-Glycosylation	Interactions Focus chain L Interactions & Density Focus chain L
Glycosylation Resources
GlyTouCan: G08466KH GlyCosmos: G08466KH GlyGen: G08466KH

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV Query on POV Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain S [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] MOL2 format, chain M [auth A] MOL2 format, chain S [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain M [auth A] mmCIF format, chain S [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C]	M [auth A], Q [auth C], R [auth C], S [auth D]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain M [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Interactions & Density Focus chain M [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D]
PLM Query on PLM Download:Ideal Coordinates CCD File SDF format, chain U [auth E] MOL2 format, chain U [auth E] mmCIF format, chain U [auth E]	U [auth E]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain U [auth E] Interactions & Density Focus chain U [auth E]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain T [auth E] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain T [auth E] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain T [auth E]	N [auth B], O [auth B], T [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain N [auth B] Focus chain O [auth B] Focus chain T [auth E] Interactions & Density Focus chain N [auth B] Focus chain O [auth B] Focus chain T [auth E]
OCT Query on OCT Download:Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]