SMTL ID : 9bly.1

Composite structure of full-length human dynein-1 in phi-particle conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-mer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 16 residues within 4Å: Chain A: L.1879, V.1880, T.1882, T.1885, P.1907, G.1909, T.1910, G.1911, K.1912, T.1913, E.1914, I.2049, L.2090, R.2091, K.2094 Ligands: MG.5 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:V.1880, A:V.1880, A:P.1907, A:G.1909, A:T.1910, A:G.1911, A:K.1912, A:T.1913, A:E.1914, A:K.2094, A:R.2358 Salt bridges: A:K.1912, A:R.2091, A:R.2091 ADP.3: 17 residues within 4Å: Chain A: V.2567, V.2568, V.2569, T.2571, T.2574, P.2596, G.2598, S.2599, G.2600, K.2601, T.2602, M.2603, I.2747, Y.2748, P.2796, R.2797, T.2800 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:V.2569, A:V.2569, A:P.2596, A:G.2598, A:S.2599, A:G.2600, A:K.2601, A:T.2602, A:T.2602, A:T.2602, A:M.2603 Salt bridges: A:K.2601, A:R.2797, A:R.2797 ADP.4: 17 residues within 4Å: Chain A: V.2907, P.2908, L.2909, V.2910, F.2912, V.2938, S.2939, G.2940, A.2941, G.2942, K.2943, T.2944, T.2945, W.3097, R.3174, L.3177, N.3650 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:V.2910, A:V.2910, A:G.2940, A:A.2941, A:G.2942, A:K.2943, A:T.2944, A:T.2944, A:T.2944, A:T.2945, A:T.2945 Salt bridges: A:K.2943 ADP.7: 16 residues within 4Å: Chain B: L.1879, V.1880, T.1882, T.1885, P.1907, G.1909, T.1910, G.1911, K.1912, T.1913, E.1914, I.2049, L.2090, R.2091, K.2094 Ligands: MG.11 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:V.1880, B:V.1880, B:T.1885, B:P.1907, B:G.1909, B:T.1910, B:G.1911, B:K.1912, B:T.1913, B:E.1914, B:E.1914, B:K.2094, B:R.2358 Salt bridges: B:K.1912, B:R.2091, B:R.2091 ADP.9: 17 residues within 4Å: Chain B: V.2567, V.2568, V.2569, T.2571, T.2574, P.2596, G.2598, S.2599, G.2600, K.2601, T.2602, M.2603, I.2747, Y.2748, P.2796, R.2797, T.2800 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:V.2569, B:V.2569, B:P.2596, B:G.2598, B:S.2599, B:G.2600, B:K.2601, B:T.2602, B:T.2602, B:M.2603, B:Y.2748, B:T.2800 Salt bridges: B:K.2601, B:R.2797, B:R.2797 ADP.10: 17 residues within 4Å: Chain B: V.2907, P.2908, L.2909, V.2910, F.2912, V.2938, S.2939, G.2940, A.2941, G.2942, K.2943, T.2944, T.2945, W.3097, R.3174, L.3177, N.3650 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:V.2910, B:V.2910, B:G.2940, B:A.2941, B:G.2942, B:K.2943, B:T.2944, B:T.2944, B:T.2945, B:T.2945 Salt bridges: B:K.2943

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 21 residues within 4Å: Chain A: L.2191, T.2192, W.2203, P.2225, S.2226, G.2227, S.2228, G.2229, K.2230, S.2231, M.2232, E.2344, L.2369, M.2373, I.2374, N.2377, L.2452, R.2684, R.2726, R.2729 Ligands: MG.6 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:T.2192, A:W.2203, A:G.2227, A:S.2228, A:G.2229, A:G.2229, A:K.2230, A:S.2231, A:M.2232 Salt bridges: A:K.2230, A:K.2230, A:R.2684, A:R.2726, A:R.2729, A:R.2729, A:R.2729 ATP.8: 21 residues within 4Å: Chain B: L.2191, T.2192, W.2203, P.2225, S.2226, G.2227, S.2228, G.2229, K.2230, S.2231, M.2232, E.2344, L.2369, M.2373, I.2374, N.2377, L.2452, R.2684, R.2726, R.2729 Ligands: MG.12 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:T.2192, B:W.2203, B:G.2227, B:S.2228, B:G.2229, B:G.2229, B:K.2230, B:S.2231, B:M.2232 Salt bridges: B:K.2230, B:K.2230, B:R.2684, B:R.2726, B:R.2729, B:R.2729, B:R.2729

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: T.1913, R.2358 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.1913 MG.6: 3 residues within 4Å: Chain A: S.2231, E.2344 Ligands: ATP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.2231, A:E.2344 MG.11: 3 residues within 4Å: Chain B: T.1913, R.2358 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.1913 MG.12: 3 residues within 4Å: Chain B: S.2231, E.2344 Ligands: ATP.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.2231, B:E.2344

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chai, P. et al., Cryo-EM Reveals the Mechanochemical Cycle of Reactive Full-length Human Dynein-1. To Be Published

Release Date

2025-04-23

Peptides

Cytoplasmic dynein 1 heavy chain 1: AB
Cytoplasmic dynein 1 intermediate chain 2: CD
Cytoplasmic dynein 1 light intermediate chain 2: EF
Dynein light chain roadblock-type 1: GH
Dynein light chain 1, cytoplasmic: IJ
Dynein light chain Tctex-type 1: KL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Cytoplasmic dynein 1 heavy chain 1

Cytoplasmic dynein 1 intermediate chain 2

Cytoplasmic dynein 1 light intermediate chain 2

Dynein light chain roadblock-type 1

Dynein light chain 1, cytoplasmic

Dynein light chain Tctex-type 1

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