9C3C | pdb_00009c3c

Cryo-EM structure of native dystrophin-glycoprotein complex (DGC)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Native DGC structure rationalizes muscular dystrophy-causing mutations.

Liu, S.Su, T.Xia, X.Zhou, Z.H.

(2025) Nature 637: 1261-1271

  • DOI: https://doi.org/10.1038/s41586-024-08324-w
  • Primary Citation of Related Structures:  
    9C3C

  • PubMed Abstract: 

    Duchenne muscular dystrophy (DMD) is a severe X-linked recessive disorder marked by progressive muscle wasting leading to premature mortality 1,2 . Discovery of the DMD gene encoding dystrophin both revealed the cause of DMD and helped identify a family of at least ten dystrophin-associated proteins at the muscle cell membrane, collectively forming the dystrophin-glycoprotein complex (DGC) 3-9 . The DGC links the extracellular matrix to the cytoskeleton, but, despite its importance, its molecular architecture has remained elusive. Here we determined the native cryo-electron microscopy structure of rabbit DGC and conducted biochemical analyses to reveal its intricate molecular configuration. An unexpected β-helix comprising β-, γ- and δ-sarcoglycan forms an extracellular platform that interacts with α-dystroglycan, β-dystroglycan and α-sarcoglycan, allowing α-dystroglycan to contact the extracellular matrix. In the membrane, sarcospan anchors β-dystroglycan to the β-, γ- and δ-sarcoglycan trimer, while in the cytoplasm, β-dystroglycan's juxtamembrane fragment binds dystrophin's ZZ domain. Through these interactions, the DGC links laminin 2 to intracellular actin. Additionally, dystrophin's WW domain, along with its EF-hand 1 domain, interacts with α-dystrobrevin. A disease-causing mutation mapping to the WW domain weakens this interaction, as confirmed by deletion of the WW domain in biochemical assays. Our findings rationalize more than 110 mutations affecting single residues associated with various muscular dystrophy subtypes and contribute to ongoing therapeutic developments, including protein restoration, upregulation of compensatory genes and gene replacement.


  • Organizational Affiliation
    • Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-dystroglycan624Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for Q28685 (Oryctolagus cuniculus)
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UniProt GroupQ28685
Glycosylation
Glycosylation Sites: 2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-dystroglycan145Oryctolagus cuniculusMutation(s): 0 
UniProt
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UniProt GroupQ28685
Glycosylation
Glycosylation Sites: 1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DystrophinC [auth D]3,696Oryctolagus cuniculusMutation(s): 0 
UniProt
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UniProt GroupG1T8Y6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-sarcoglycanD [auth a]326Oryctolagus cuniculusMutation(s): 0 
UniProt
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UniProt GroupQ28686
Glycosylation
Glycosylation Sites: 2
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-sarcoglycanE [auth b]318Oryctolagus cuniculusMutation(s): 0 
UniProt
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UniProt GroupQ28635
Glycosylation
Glycosylation Sites: 3
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Sarcoglycan deltaF [auth d]289Oryctolagus cuniculusMutation(s): 0 
UniProt
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UniProt GroupG1SGL0
Glycosylation
Glycosylation Sites: 1
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-sarcoglycanG [auth g]291Oryctolagus cuniculusMutation(s): 0 
UniProt
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UniProt GroupQ28646
Glycosylation
Glycosylation Sites: 1
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
SarcospanH [auth n]238Oryctolagus cuniculusMutation(s): 0 
UniProt
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UniProt GroupP82352
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DystrobrevinI [auth V]818Oryctolagus cuniculusMutation(s): 0 
UniProt
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UniProt GroupA0A5F9C316
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Oligosaccharides

Help

Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J [auth H],
K,
L [auth O],
M [auth R],
N [auth C],
J [auth H],
K,
L [auth O],
M [auth R],
N [auth C],
O [auth E],
P [auth F]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 11
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseQ [auth G]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM071940

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-23
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection
  • Version 1.2: 2024-12-25
    Changes: Data collection, Database references
  • Version 1.3: 2025-02-12
    Changes: Data collection, Database references