SMTL ID : 9c3c.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-mer

Ligands

7 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 6 residues within 4Å: Chain A: F.608, D.610, T.615, V.616 Chain B: N.8, T.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.610 NAG-NAG-BMA.2: 6 residues within 4Å: Chain D: R.50, R.53, A.68, N.150, T.152, K.175 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 4 residues within 4Å: Chain E: N.134 Chain F: N.108, K.129, E.132 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:K.129 NAG-NAG-BMA.4: 5 residues within 4Å: Chain F: N.99, A.100 Chain G: Q.109, N.110, K.127 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 2 residues within 4Å: Chain A: N.620, T.622 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 16 residues within 4Å: Chain A: V.64, I.65, K.66, V.67, S.68, E.73, V.74, L.75, W.81, P.83, H.86 Chain E: N.258 Chain F: P.243, R.244 Chain G: H.229, S.231 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.73, A:L.75, A:W.81, A:I.65, A:V.67, A:W.81 Hydrophobic interactions: A:V.64, A:I.65, A:P.83 NAG-NAG-BMA.7: 3 residues within 4Å: Chain E: N.211, T.213, S.214 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.8: 4 residues within 4Å: Chain E: E.156, N.158, K.159 Chain F: K.137 No protein-ligand interaction detected (PLIP)

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.9: 2 residues within 4Å: Chain A: N.612, S.614 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.614 NAG.10: 2 residues within 4Å: Chain D: C.221, N.222 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, S. et al., Native DGC Structure Rationalizes Muscular Dystrophy-Causing Mutations. To Be Published

Release Date

2024-10-23

Peptides

Alpha-dystroglycan: A
Beta-dystroglycan: B
Dystrophin: C
Alpha-sarcoglycan: D
Beta-sarcoglycan: E
Sarcoglycan delta: F
Gamma-sarcoglycan: G
Sarcospan: H
Dystrobrevin: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
a

E
b

F
d

G
g

H
n

I
V

Membrane

We predict this structure to be a membrane protein.
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Alpha-dystroglycan

Beta-dystroglycan

Dystrophin

Alpha-sarcoglycan

Beta-sarcoglycan

Sarcoglycan delta

Gamma-sarcoglycan

Sarcospan

Dystrobrevin