7SMQ

Cryo-EM structure of Torpedo acetylcholine receptor in apo form with added cholesterol

PDB DOI: https://doi.org/10.2210/pdb7SMQ/pdb
EM Map EMD-25205: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Tetronarce californica
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2021-10-26 Released: 2022-03-09
Deposition Author(s): Rahman, M.M., Basta, T., Teng, J., Lee, M., Worrell, B.T., Stowell, M.H.B., Hibbs, R.E.
Funding Organization(s): National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.74 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 283.55 kDa
Atom Count: 17,427
Modelled Residue Count: 2,030
Deposited Residue Count: 2,333
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02710
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02718
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02712
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02714
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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	F, I	7	N/A	N-Glycosylation	Interactions Focus chain F Focus chain I Interactions & Density Focus chain F Focus chain I
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	3	N/A	N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	2	N/A	N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J	5	N/A	N-Glycosylation	Interactions Focus chain J Interactions & Density Focus chain J
Glycosylation Resources
GlyTouCan: G94626GC GlyCosmos: G94626GC GlyGen: G94626GC

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 AA [auth D] SDF format, chain BA [auth D] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain X [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain X [auth D]	AA [auth D] BA [auth D] DA [auth E] EA [auth E] K [auth A] AA [auth D], BA [auth D], DA [auth E], EA [auth E], K [auth A], P [auth B], Q [auth B], X [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 AA [auth D] Focus chain BA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain X [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain X [auth D]
CLR (Subject of Investigation/LOI) Query on CLR Download Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain GA [auth E] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	FA [auth E] GA [auth E] L [auth A] M [auth A] R [auth B] FA [auth E], GA [auth E], L [auth A], M [auth A], R [auth B], S [auth B], U [auth C], V [auth C], W [auth C], Y [auth D], Z [auth D]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain FA [auth E] Focus chain GA [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain FA [auth E] Focus chain GA [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain CA [auth E] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	CA [auth E], N [auth B], O [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CA [auth E] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain CA [auth E] Focus chain N [auth B] Focus chain O [auth B]
DD9 Query on DD9 Download Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B]	T [auth B]	nonane C₉ H₂₀ BKIMMITUMNQMOS-UHFFFAOYSA-N		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]