9DML | pdb_00009dml

Human muscle nAChR with fab2-bound


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.24 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


Literature

Autoimmune mechanisms elucidated through muscle acetylcholine receptor structures.

Li, H.Pham, M.C.Teng, J.O'Connor, K.C.Noviello, C.M.Hibbs, R.E.

(2025) Cell 188: 2390-2406.e20

  • DOI: https://doi.org/10.1016/j.cell.2025.03.004
  • Primary Citation of Related Structures:  
    9DMG, 9DMH, 9DMJ, 9DMK, 9DML, 9DMQ, 9DMS, 9DMT

  • PubMed Abstract: 

    Skeletal muscle contraction is triggered by acetylcholine (ACh) binding to its ionotropic receptors (AChRs) at neuromuscular junctions. In myasthenia gravis (MG), autoantibodies target AChRs, disrupting neurotransmission and causing muscle weakness. While treatments exist, variable patient responses suggest pathogenic heterogeneity. Progress in understanding the molecular basis of MG has been limited by the absence of structures of intact human muscle AChRs. Here, we present high-resolution cryoelectron microscopy (cryo-EM) structures of the human adult AChR in different functional states. Using six MG patient-derived monoclonal antibodies, we mapped distinct epitopes involved in diverse pathogenic mechanisms, including receptor blockade, internalization, and complement activation. Electrophysiological and binding assays revealed how these autoantibodies directly inhibit AChR channel activation. These findings provide critical insights into MG immunopathogenesis, uncovering unrecognized antibody epitope diversity and modes of receptor inhibition, and provide a framework for developing personalized therapies targeting antibody-mediated autoimmune disorders.


  • Organizational Affiliation
    • Department of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab2 heavy chain
A, B
273Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab2 light chain
C, D
234Homo sapiensMutation(s): 0 
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Glycosylation
Glycosylation Sites: 1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Acetylcholine receptor subunit alpha
E, F
457Homo sapiensMutation(s): 0 
Gene Names: CHRNA1ACHRACHNRA
UniProt & NIH Common Fund Data Resources
Find proteins for P02708 (Homo sapiens)
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Go to UniProtKB:  P02708
PHAROS:  P02708
GTEx:  ENSG00000138435 
Entity Groups  
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UniProt GroupP02708
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P02708-2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Acetylcholine receptor subunit beta503Homo sapiensMutation(s): 0 
Gene Names: CHRNB1ACHRBCHRNB
UniProt & NIH Common Fund Data Resources
Find proteins for P11230 (Homo sapiens)
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Go to UniProtKB:  P11230
PHAROS:  P11230
GTEx:  ENSG00000170175 
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UniProt GroupP11230
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P11230-1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Acetylcholine receptor subunit delta517Homo sapiensMutation(s): 0 
Gene Names: CHRNDACHRD
UniProt & NIH Common Fund Data Resources
Find proteins for Q07001 (Homo sapiens)
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Go to UniProtKB:  Q07001
PHAROS:  Q07001
GTEx:  ENSG00000135902 
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UniProt GroupQ07001
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q07001-1
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Acetylcholine receptor subunit epsilon493Homo sapiensMutation(s): 0 
Gene Names: CHRNEACHRE
UniProt & NIH Common Fund Data Resources
Find proteins for Q04844 (Homo sapiens)
Explore Q04844 
Go to UniProtKB:  Q04844
PHAROS:  Q04844
GTEx:  ENSG00000108556 
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UniProt GroupQ04844
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q04844-1
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Oligosaccharides

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Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D 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
J, K, L, M
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D 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
N
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV
Query on POV

Download Ideal Coordinates CCD File 
Q [auth H],
R [auth H]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
T [auth I],
U [auth I]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
O [auth C],
P [auth D],
S [auth I]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Data collection
  • Version 1.2: 2025-10-22
    Changes: Data collection, Database references