SMTL ID : 7kek.1

Structure of the free outer-arm dynein in pre-parallel state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: L.2459, L.2460, L.2461, T.2463, G.2494, G.2496, T.2497, A.2498, K.2499, T.2500, S.2501, L.2505, Y.2644, M.2696, R.2697 Ligands: MG.5 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:L.2461, A:L.2461, A:T.2463, A:G.2496, A:T.2497, A:A.2498, A:K.2499, A:T.2500, A:S.2501, A:S.2501, A:S.2700 Salt bridges: A:K.2499, A:R.2697, A:R.2697 ADP.3: 15 residues within 4Å: Chain A: P.2838, L.2839, V.2840, F.2842, G.2869, G.2870, S.2871, G.2872, K.2873, Q.2874, S.2875, W.3030, V.3038, L.3093 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:V.2840, A:V.2840, A:G.2870, A:S.2871, A:G.2872, A:G.2872, A:K.2873, A:Q.2874, A:Q.2874, A:S.2875 Salt bridges: A:K.2873 ADP.9: 14 residues within 4Å: Chain B: T.1983, V.1984, S.2012, G.2013, G.2015, K.2016, T.2017, Q.2018, N.2129, I.2161, L.2212, R.2213, N.2508 Ligands: MG.10 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:V.1984, B:V.1984, B:G.2015, B:K.2016, B:T.2017, B:N.2508 Salt bridges: B:K.2016, B:R.2213, B:R.2213 ADP.12: 11 residues within 4Å: Chain B: M.2330, L.2332, G.2362, G.2363, S.2364, G.2365, K.2366, Q.2367, S.2368, L.2579 Ligands: MG.11 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.2364, B:G.2365, B:G.2365, B:K.2366, B:Q.2367, B:S.2368 Salt bridges: B:K.2366 ADP.17: 14 residues within 4Å: Chain D: I.2510, Y.2511, V.2512, A.2540, G.2541, T.2542, G.2543, K.2544, T.2545, A.2546, I.2687, F.2741, R.2742 Ligands: MG.15 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:S.2508, D:V.2512, D:V.2512, D:A.2540, D:A.2540, D:G.2543, D:K.2544, D:T.2545, D:T.2545, D:A.2546 Salt bridges: D:K.2544, D:R.2742, D:R.2742 ADP.18: 14 residues within 4Å: Chain D: M.2860, L.2862, V.2863, F.2865, G.2892, G.2893, S.2894, G.2895, K.2896, Q.2897, S.2898, W.3051, L.3112 Ligands: MG.16 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:V.2863, D:G.2893, D:S.2894, D:G.2895, D:K.2896, D:Q.2897, D:S.2898 Salt bridges: D:K.2896

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

ATP.2: 21 residues within 4Å: Chain A: Y.2129, L.2130, I.2131, F.2136, P.2158, T.2159, G.2160, S.2161, G.2162, K.2163, S.2164, T.2165, E.2273, L.2298, A.2302, V.2303, H.2483, E.2584, R.2624, R.2627 Ligands: MG.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:I.2131, A:I.2131, A:G.2160, A:S.2161, A:G.2162, A:K.2163, A:S.2164, A:S.2164, A:T.2165, A:T.2165, A:E.2273 Salt bridges: A:K.2163, A:K.2163, A:R.2624, A:R.2627, A:R.2627, A:R.2627 ATP.7: 19 residues within 4Å: Chain B: L.1657, D.1658, F.1663, P.1686, G.1687, A.1688, G.1689, K.1690, S.1691, T.1692, E.1799, S.1829, Y.1830, S.1833, R.2100, D.2104, R.2140, R.2143 Ligands: MG.8 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:D.1658, B:G.1687, B:G.1689, B:K.1690, B:S.1691, B:T.1692, B:S.1829, B:S.1833, B:R.2100, B:R.2140 Salt bridges: B:R.2140, B:R.2143, B:R.2143, B:R.2143 ATP.13: 22 residues within 4Å: Chain D: L.2157, V.2158, F.2163, P.2186, G.2187, S.2188, G.2189, K.2190, T.2191, C.2192, E.2304, I.2329, P.2333, Y.2334, S.2337, Q.2343, I.2399, Q.2403, R.2625, R.2666, R.2669 Ligands: MG.14 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:V.2158, D:V.2158, D:S.2188, D:K.2190, D:T.2191, D:T.2191, D:C.2192, D:E.2304, D:Q.2343, D:Q.2403 Salt bridges: D:K.2190, D:R.2666, D:R.2669, D:R.2669, D:R.2669

9 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: S.2164, E.2273, E.2584 Ligands: ATP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.2164, A:E.2273 MG.5: 4 residues within 4Å: Chain A: T.2500, D.2560, R.2697 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.2500 MG.6: 3 residues within 4Å: Chain A: G.2869, G.2870 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain B: S.1691, D.1759, D.2104, R.2140 Ligands: ATP.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.1691, B:D.2104 MG.10: 3 residues within 4Å: Chain B: T.2017, R.2213 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.2017 MG.11: 2 residues within 4Å: Chain B: G.2362 Ligands: ADP.12 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.2362 MG.14: 5 residues within 4Å: Chain D: T.2191, E.2304, D.2629, R.2669 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.2304 MG.15: 3 residues within 4Å: Chain D: T.2545, D.2605 Ligands: ADP.17 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.2545 MG.16: 4 residues within 4Å: Chain D: K.2896, Q.2897, T.2949 Ligands: ADP.18 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rao, Q. et al., Structures of outer-arm dynein array on microtubule doublet reveal a motor coordination mechanism. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-09-29

Peptides

Dynein alpha heavy chain: A
Dynein gamma heavy chain: B
Dynein light chain 1: C
Dynein beta heavy chain: D
Dynein light chain LC8_1a (LC10): E
Dynein light chain LC8_1b (DLC82): F
Dynein light chain roadblock LC7B: G
Dynein light chain roadblock LC7A: H
Dynein light chain Tctex_b: I
Dynein light chain Tctex_a (LC2A): J
Dynein intermediate chain DIC3: K
Dynein intermediate chain DIC2: L
Thioredoxin LC3BL: M
Dynein light chain LC8_3b: N
Dynein light chain LC8_2a (LC8E): O
Dynein light chain LC8_2b: P
Dynein light chain LC8_3a: Q

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
Q

D
B

E
I

F
H

G
G

H
F

I
N

J
O

K
E

L
D

M
P

N
L

O
K

P
J

Q
M

Dynein alpha heavy chain

Dynein gamma heavy chain

Dynein light chain 1

Dynein beta heavy chain

Dynein light chain LC8_1a (LC10)

Dynein light chain LC8_1b (DLC82)

Dynein light chain roadblock LC7B

Dynein light chain roadblock LC7A

Dynein light chain Tctex_b

Dynein light chain Tctex_a (LC2A)

Dynein intermediate chain DIC3

Dynein intermediate chain DIC2

Thioredoxin LC3BL

Dynein light chain LC8_3b

Dynein light chain LC8_2a (LC8E)

Dynein light chain LC8_2b

Dynein light chain LC8_3a

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