SMTL ID : 7k5b.1

Structure of outer-arm dynein bound to microtubule doublet in microtubule binding state 2 (MTBS-2)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: L.2455, L.2456, L.2457, T.2459, G.2492, T.2493, A.2494, K.2495, T.2496, S.2497, Y.2640, M.2692, R.2693, S.2696 Ligands: MG.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:L.2457, A:L.2457, 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: L.2835, V.2836, F.2838, A.2841, G.2865, G.2866, S.2867, G.2868, K.2869, Q.2870, S.2871, W.3026, K.3086, L.3089 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:P.2834, 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.10: 12 residues within 4Å: Chain B: I.2510, Y.2511, V.2512, A.2540, T.2542, G.2543, K.2544, T.2545, A.2546, R.2742, N.3041 Ligands: MG.8 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:V.2512, B:V.2512, B:G.2543, B:T.2545, B:T.2545, B:A.2546, B:R.2742 Salt bridges: B:K.2544, B:K.2544, B:R.2742, B:R.2742 ADP.12: 15 residues within 4Å: Chain B: N.2861, L.2862, V.2863, F.2865, V.2891, G.2892, G.2893, S.2894, G.2895, K.2896, Q.2897, S.2898, W.3051, L.3112 Ligands: MG.9 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:V.2863, B:V.2891, B:G.2893, B:S.2894, B:G.2895, B:K.2896, B:Q.2897, B:Q.2897, B:S.2898 Salt bridges: B:K.2896 ADP.17: 12 residues within 4Å: Chain C: T.1866, V.1867, G.1896, C.1897, K.1899, T.1900, Q.1901, L.1902, N.2012, R.2096, N.2391 Ligands: MG.15 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:V.1867, C:T.1900, C:T.1900, C:Q.1901, C:Q.1901, C:N.2012, C:N.2391 Salt bridges: C:K.1899, C:K.1899, C:R.2096, C:R.2096 ADP.18: 10 residues within 4Å: Chain C: M.2213, G.2243, G.2245, G.2246, G.2248, K.2249, Q.2250, S.2251, L.2252 Ligands: MG.16 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.2243, C:Q.2250, C:S.2251, C:S.2251, C:L.2252 Salt bridges: C:K.2249

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

ATP.2: 22 residues within 4Å: Chain A: Y.2125, L.2126, I.2127, F.2132, T.2155, G.2156, S.2157, G.2158, K.2159, S.2160, T.2161, E.2269, L.2294, A.2298, V.2299, G.2302, H.2479, T.2480, 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:T.2161, A:T.2161, A:E.2269, A:R.2620 Salt bridges: A:K.2159, A:K.2159, A:R.2620, A:R.2623, A:R.2623, A:R.2623 ATP.11: 21 residues within 4Å: Chain B: L.2157, V.2158, P.2185, P.2186, G.2187, S.2188, G.2189, K.2190, T.2191, C.2192, E.2304, P.2333, Y.2334, S.2337, Q.2343, I.2399, Q.2403, R.2625, R.2666, R.2669 Ligands: MG.7 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:V.2158, B:P.2185, B:S.2188, B:K.2190, B:T.2191, B:C.2192, B:E.2304, B:S.2337 Salt bridges: B:K.2190, B:K.2190, B:R.2666, B:R.2669, B:R.2669, B:R.2669 ATP.13: 17 residues within 4Å: Chain C: L.1540, D.1541, F.1546, P.1569, G.1570, A.1571, G.1572, K.1573, S.1574, T.1575, S.1712, Y.1713, S.1716, R.1983, R.2023, R.2026 Ligands: MG.14 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:D.1541, C:D.1541, C:G.1570, C:G.1572, C:K.1573, C:S.1574, C:S.1574, C:T.1575, C:S.1712, C:S.1716, C:R.1983 Salt bridges: C:R.2023, C:R.2026, C:R.2026

9 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: S.2160, E.2580, R.2623 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.2160 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: 4 residues within 4Å: Chain A: G.2865, G.2866, K.3086 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain B: T.2191, D.2629, R.2669 Ligands: ATP.11 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: T.2545, D.2605, R.2742 Ligands: ADP.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.2545 MG.9: 2 residues within 4Å: Chain B: Q.2897 Ligands: ADP.12 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain C: S.1574, R.2023 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.1574 MG.15: 3 residues within 4Å: Chain C: T.1900, D.1963 Ligands: ADP.17 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.1900 MG.16: 4 residues within 4Å: Chain C: G.2245, G.2246, K.2459 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
Outer arm dynein beta heavy chain: B
gamma heavy chain: C
Dynein intermediate chain 2: D
Flagellar outer dynein arm intermediate protein, putative: E
Dynein light chain roadblock-type 2 protein: F
Dynein light chain roadblock-type 2 protein: G
Dynein light chain: H
Dynein light chain: I
Dynein light chain: J
Dynein light chain: K
Dynein light chain: L
Dynein light chain: M
Dynein light chain tctex-type 1 protein: N
Dynein light chain 2A: O
Thioredoxin: P
Dynein light chain 1: Q
Dynein light chain 4A: R

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

M
M

N
N

O
O

P
P

Q
Q

R
R

Dynein heavy chain, outer arm protein

Outer arm dynein beta heavy chain

gamma heavy chain

Dynein intermediate chain 2

Flagellar outer dynein arm intermediate protein, putative

Dynein light chain roadblock-type 2 protein

Dynein light chain roadblock-type 2 protein

Dynein light chain

Dynein light chain

Dynein light chain

Dynein light chain

Dynein light chain

Dynein light chain

Dynein light chain tctex-type 1 protein

Dynein light chain 2A

Thioredoxin

Dynein light chain 1

Dynein light chain 4A

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