9DMV | pdb_00009dmv

Human muscle nAChR with fab9-bound

PDB DOI: https://doi.org/10.2210/pdb9DMV/pdb
EM Map EMD-47017: EMDB EMDataResource

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

Deposited: 2024-09-14 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: 2.13 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 human muscle AChR with fab9-bound

Li, H., Hibbs, R.E.

To be published.

Macromolecule Content

Total Structure Weight: 338.87 kDa
Atom Count: 20,424
Modeled Residue Count: 2,475
Deposited Residue Count: 2,925
Unique protein chains: 6

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholine receptor subunit beta	C [auth E]	502	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q07001
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain D	Go to GlyGen: Q07001-1
Sequence Annotations Expand
Reference Sequence

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q04844
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain E [auth B]	Go to GlyGen: Q04844-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab9 heavy chain	F	266	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab9 light chain	G	233	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	H, I, J, K	5		N-Glycosylation	Interactions Focus chain H Focus chain I Focus chain J Focus chain K Interactions & Density Focus chain H Focus chain I Focus chain J Focus chain K
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	L	4		N-Glycosylation	Interactions Focus chain L Interactions & Density Focus chain L
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M	2		N-Glycosylation	Interactions Focus chain M Interactions & Density Focus chain M
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 N [auth A] SDF format, chain R [auth D] SDF format, chain U [auth D] SDF format, chain X [auth B] MOL2 format, chain N [auth A] MOL2 format, chain R [auth D] MOL2 format, chain U [auth D] MOL2 format, chain X [auth B] mmCIF format, chain N [auth A] mmCIF format, chain R [auth D] mmCIF format, chain U [auth D] mmCIF format, chain X [auth B]	N [auth A], R [auth D], U [auth D], X [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 N [auth A] Focus chain R [auth D] Focus chain U [auth D] Focus chain X [auth B] Interactions & Density Focus chain N [auth A] Focus chain R [auth D] Focus chain U [auth D] Focus chain X [auth B]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain O [auth E] SDF format, chain Q [auth D] SDF format, chain T [auth D] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain S [auth D] MOL2 format, chain O [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain T [auth D] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain S [auth D] mmCIF format, chain O [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain T [auth D] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain S [auth D]	O [auth E] Q [auth D] S [auth D] T [auth D] V [auth B] O [auth E], Q [auth D], S [auth D], T [auth D], V [auth B], W [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain O [auth E] Focus chain Q [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain O [auth E] Focus chain Q [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth B] Focus chain W [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain P [auth D] MOL2 format, chain P [auth D] mmCIF format, chain P [auth D]	P [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain P [auth D] Interactions & Density Focus chain P [auth D]