SMTL ID : 8yt8.1

Cryo-EM structure of the dystrophin glycoprotein complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ALA- LEU- PRO- LYS- MET: unknown segment(Non-covalent)

ALA-LEU-PRO-LYS-MET.1: 14 residues within 4Å: Chain B: T.3, G.4, R.6, K.9 Chain E: K.237, Q.239 Chain F: R.8, Y.11, L.15 Chain G: G.275, A.278, Y.282 Chain H: W.168, Y.172 9 PLIP interactions: 3 interactions with chain G, 1 interactions with chain H, 3 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: G:A.278, H:Y.172, B:T.3, B:K.9 Hydrogen bonds: G:Y.282, G:Y.282, B:R.6, E:K.237, E:K.237

5 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.2: 3 residues within 4Å: Chain A: R.51, N.151, K.176 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.51 NAG-NAG-BMA.5: 2 residues within 4Å: Chain B: N.159, S.162 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 4 residues within 4Å: Chain B: I.204, N.206 Chain D: R.218 Chain F: Q.203 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 4 residues within 4Å: Chain B: N.82 Chain D: N.82, V.99, K.103 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 6 residues within 4Å: Chain D: A.74, Y.76 Chain F: Q.83, N.84, R.99, K.101 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 5 residues within 4Å: Chain A: C.199, A.200, D.220, C.222, N.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.200

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

NAG-NAG.4: 2 residues within 4Å: Chain B: N.106, K.107 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain G: N.148, S.150 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.9: 9 residues within 4Å: Chain G: F.144, G.145, D.146, S.151, I.152, N.168, T.170, L.171, R.187 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:F.144

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

NAG.11: 2 residues within 4Å: Chain A: T.256, E.257 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.257, B:R.79 NAG.12: 2 residues within 4Å: Chain A: P.239, T.240 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.239 Hydrogen bonds: A:T.240 NAG.17: 3 residues within 4Å: Chain G: N.156, I.157, T.158 No protein-ligand interaction detected (PLIP)

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.13: 6 residues within 4Å: Chain D: F.35, T.36, I.37 Chain G: Y.257, A.268 Ligands: CLR.14 4 PLIP interactions: 1 interactions with chain G, 3 interactions with chain D Hydrophobic interactions: G:A.268, D:I.37 Hydrogen bonds: D:T.36, D:I.37 CLR.14: 6 residues within 4Å: Chain D: I.27, K.31, F.35 Chain F: I.20, V.23 Ligands: CLR.13 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:I.27, D:K.31, F:I.20, F:V.23 Hydrogen bonds: D:N.34 CLR.19: 6 residues within 4Å: Chain H: F.70, V.74, F.77, M.167, H.170, R.171 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:F.70, H:M.167, H:H.170, H:R.171

1 x ZN: ZINC ION(Non-covalent)

ZN.15: 5 residues within 4Å: Chain E: C.242, C.245, C.266, C.269, R.274 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.242, E:C.245, E:C.266, E:C.269

1 x P5S: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)

P5S.16: 7 residues within 4Å: Chain A: I.288 Chain E: N.262, D.264, F.301 Chain F: W.5, R.6, C.9 4 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: F:W.5, E:N.262 Salt bridges: F:R.6 Hydrophobic interactions: A:I.288

1 x CA: CALCIUM ION(Non-covalent)

CA.18: 6 residues within 4Å: Chain B: E.178 Chain F: T.172 Chain G: H.9, D.11, D.96, A.97 5 PLIP interactions: 3 interactions with chain G, 1 interactions with chain F, 1 interactions with chain B Metal complexes: G:H.9, G:D.11, G:D.96, F:T.172, B:E.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, J.P. et al., Structure and assembly of the dystrophin glycoprotein complex. Nature (2024)

Release Date

2024-12-11

Peptides

Alpha-sarcoglycan: A
Beta-sarcoglycan: B
Dystrobrevin alpha: C
Delta-sarcoglycan: D
Dystrophin: E
Gamma-sarcoglycan: F
Beta-dystroglycan: G
Sarcospan: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
G

G
O

H
S

Membrane

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

Beta-sarcoglycan

Dystrobrevin alpha

Delta-sarcoglycan

Dystrophin

Gamma-sarcoglycan

Beta-dystroglycan

Sarcospan