9DMG | pdb_00009dmg

Human muscle nAChR apo state

PDB DOI: https://doi.org/10.2210/pdb9DMG/pdb
EM Map EMD-47003: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2024-09-13 Released: 2025-04-09
Deposition Author(s): Li, H., Hibbs, R.E.
Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.05 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structure of human muscle AChR apo state

Li, H., Hibbs, R.E.

To be published.

Macromolecule Content

Total Structure Weight: 285.71 kDa
Atom Count: 17,223
Modelled Residue Count: 2,049
Deposited Residue Count: 2,427
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, B [auth C]	457	Homo sapiens	Mutation(s): 0 Gene Names: CHRNA1, ACHRA, CHNRA Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P02708 (Homo sapiens) Explore P02708 Go to UniProtKB: P02708
PHAROS: P02708 GTEx: ENSG00000138435
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02708
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B [auth C]	Go to GlyGen: P02708-2
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 beta	C [auth E]	503	Homo sapiens	Mutation(s): 0 Gene Names: CHRNB1, ACHRB, CHRNB Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P11230 (Homo sapiens) Explore P11230 Go to UniProtKB: P11230
PHAROS: P11230 GTEx: ENSG00000170175
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11230
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C [auth E]	Go to GlyGen: P11230-1
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 delta	D	517	Homo sapiens	Mutation(s): 0 Gene Names: CHRND, ACHRD Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q07001 (Homo sapiens) Explore Q07001 Go to UniProtKB: Q07001
PHAROS: Q07001 GTEx: ENSG00000135902
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q07001
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain D	Go to GlyGen: Q07001-1
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 epsilon	E [auth B]	493	Homo sapiens	Mutation(s): 0 Gene Names: CHRNE, ACHRE Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q04844 (Homo sapiens) Explore Q04844 Go to UniProtKB: Q04844
PHAROS: Q04844 GTEx: ENSG00000108556
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q04844
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain E [auth B]	Go to GlyGen: Q04844-1
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-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	6		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[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	G, H, I	5		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Interactions & Density Focus chain G Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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	J	2		N-Glycosylation	Interactions Focus chain J Interactions & Density Focus chain J
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-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	K	6		N-Glycosylation	Interactions Focus chain K Interactions & Density Focus chain K

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV Query on POV Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain Q [auth E] SDF format, chain T [auth D] SDF format, chain W [auth B] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth E] MOL2 format, chain T [auth D] MOL2 format, chain W [auth B] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth E] mmCIF format, chain T [auth D] mmCIF format, chain W [auth B]	L [auth A], Q [auth E], T [auth D], W [auth B]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain L [auth A] Focus chain Q [auth E] Focus chain T [auth D] Focus chain W [auth B] Interactions & Density Focus chain L [auth A] Focus chain Q [auth E] Focus chain T [auth D] Focus chain W [auth B]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain O [auth E] SDF format, chain P [auth E] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth E] mmCIF format, chain P [auth E] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	N [auth C] O [auth E] P [auth E] R [auth D] S [auth D] N [auth C], O [auth E], P [auth E], R [auth D], S [auth D], U [auth B], V [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain N [auth C] Focus chain O [auth E] Focus chain P [auth E] Focus chain R [auth D] Focus chain S [auth D] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain N [auth C] Focus chain O [auth E] Focus chain P [auth E] Focus chain R [auth D] Focus chain S [auth D] Focus chain U [auth B] Focus chain V [auth B]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]