SMTL ID : 7k58.1

Structure of outer-arm dyneins bound to microtubule with microtubule binding state 1(MTBS-1)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.50 Å

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.2455, L.2456, L.2457, T.2459, G.2490, G.2492, T.2493, A.2494, K.2495, T.2496, S.2497, L.2501, Y.2640, M.2692, R.2693 Ligands: MG.5 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:L.2457, A:L.2457, A:G.2492, A:T.2493, A:A.2494, A:K.2495, A:T.2496, A:S.2497, A:S.2497, A:S.2696 Salt bridges: A:K.2495, A:R.2693, A:R.2693 ADP.3: 15 residues within 4Å: Chain A: P.2834, L.2835, V.2836, F.2838, G.2865, G.2866, S.2867, G.2868, K.2869, Q.2870, S.2871, W.3026, V.3034, L.3089 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:V.2836, A:V.2836, A:G.2866, A:S.2867, A:G.2868, A:G.2868, A:K.2869, A:Q.2870, A:Q.2870, A:S.2871 Salt bridges: A:K.2869 ADP.9: 14 residues within 4Å: Chain B: T.1862, V.1863, S.1891, G.1892, G.1894, K.1895, T.1896, Q.1897, N.2008, I.2040, L.2091, R.2092, N.2387 Ligands: MG.10 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:V.1863, B:V.1863, B:G.1894, B:K.1895, B:T.1896, B:N.2387 Salt bridges: B:K.1895, B:R.2092, B:R.2092 ADP.12: 11 residues within 4Å: Chain B: M.2209, L.2211, G.2241, G.2242, S.2243, G.2244, K.2245, Q.2246, S.2247, L.2458 Ligands: MG.11 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.2243, B:G.2244, B:G.2244, B:K.2245, B:Q.2246, B:S.2247 Salt bridges: B:K.2245 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.2125, L.2126, I.2127, F.2132, P.2154, T.2155, G.2156, S.2157, G.2158, K.2159, S.2160, T.2161, E.2269, L.2294, A.2298, V.2299, H.2479, E.2580, R.2620, R.2623 Ligands: MG.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:I.2127, A:I.2127, A:G.2156, A:S.2157, A:G.2158, A:K.2159, A:S.2160, A:S.2160, A:T.2161, A:T.2161, A:E.2269 Salt bridges: A:K.2159, A:K.2159, A:R.2620, A:R.2623, A:R.2623, A:R.2623 ATP.7: 19 residues within 4Å: Chain B: L.1536, D.1537, F.1542, P.1565, G.1566, A.1567, G.1568, K.1569, S.1570, T.1571, E.1678, S.1708, Y.1709, S.1712, R.1979, D.1983, R.2019, R.2022 Ligands: MG.8 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:D.1537, B:G.1566, B:G.1568, B:K.1569, B:S.1570, B:T.1571, B:S.1708, B:S.1712, B:R.1979, B:R.2019 Salt bridges: B:R.2019, B:R.2022, B:R.2022, B:R.2022 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.2160, E.2269, E.2580 Ligands: ATP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.2160, A:E.2269 MG.5: 4 residues within 4Å: Chain A: T.2496, D.2556, R.2693 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.2496 MG.6: 3 residues within 4Å: Chain A: G.2865, G.2866 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain B: S.1570, D.1638, D.1983, R.2019 Ligands: ATP.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.1570, B:D.1983 MG.10: 3 residues within 4Å: Chain B: T.1896, R.2092 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.1896 MG.11: 2 residues within 4Å: Chain B: G.2241 Ligands: ADP.12 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.2241 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 heavy chain, outer arm protein: A
gamma heavy chain: B
Dynein light chain 1: C
Outer arm dynein beta heavy chain: D
Dynein light chain: E
Dynein light chain: F
Dynein light chain roadblock: G
Dynein light chain roadblock-type 2 protein: H
Dynein light chain tctex-type 1 protein: I
Dynein light chain 2A: J
Flagellar outer dynein arm intermediate protein, putative: K
Dynein intermediate chain 2: L
Thioredoxin: M
Dynein light chain: N
Dynein light chain: O
Dynein light chain: P
Dynein light chain: 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 heavy chain, outer arm protein

gamma heavy chain

Dynein light chain 1

Outer arm dynein beta heavy chain

Dynein light chain

Dynein light chain

Dynein light chain roadblock

Dynein light chain roadblock-type 2 protein

Dynein light chain tctex-type 1 protein

Dynein light chain 2A

Flagellar outer dynein arm intermediate protein, putative

Dynein intermediate chain 2

Thioredoxin

Dynein light chain

Dynein light chain

Dynein light chain

Dynein light chain

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