SMTL ID : 8bx8.1

In situ outer dynein arm from Chlamydomonas reinhardtii in the post-power stroke state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: L.2459, L.2460, L.2461, T.2463, G.2496, T.2497, A.2498, K.2499, T.2500, S.2501, Y.2644, M.2696, R.2697, S.2700 Ligands: MG.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:L.2461, A:L.2461, 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: L.2839, V.2840, F.2842, A.2845, G.2869, G.2870, S.2871, G.2872, K.2873, Q.2874, S.2875, W.3030, K.3090, L.3093 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:P.2838, A:V.2840, A:V.2840, A:G.2870, A:S.2871, A:G.2872, A:K.2873, A:Q.2874, A:Q.2874, A:S.2875, A:S.2875 Salt bridges: A:K.2873 ADP.11: 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.10 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.7 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:V.2863, B:V.2891, B:G.2893, B:S.2894, B:G.2895, 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.1983, V.1984, G.2013, C.2014, K.2016, T.2017, Q.2018, L.2019, N.2129, R.2213, N.2508 Ligands: MG.15 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:T.1983, C:V.1984, C:T.2017, C:T.2017, C:Q.2018, C:N.2129, C:N.2129, C:N.2508 Salt bridges: C:K.2016, C:K.2016, C:R.2213, C:R.2213 ADP.18: 10 residues within 4Å: Chain C: M.2330, G.2360, G.2362, G.2363, G.2365, K.2366, Q.2367, S.2368, L.2369 Ligands: MG.16 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.2360, C:Q.2367, C:S.2368, C:S.2368, C:L.2369 Salt bridges: C:K.2366

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

ATP.2: 22 residues within 4Å: Chain A: Y.2129, L.2130, I.2131, F.2136, T.2159, G.2160, S.2161, G.2162, K.2163, S.2164, T.2165, E.2273, L.2298, A.2302, V.2303, G.2306, H.2483, T.2484, E.2584, R.2624, R.2627 Ligands: MG.4 16 PLIP interactions: 16 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:T.2165, A:T.2165, A:R.2624 Salt bridges: A:K.2163, A:K.2163, A:R.2624, A:R.2627, A:R.2627, A:R.2627 ATP.9: 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.8 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:V.2158, B:V.2158, B:P.2185, B:S.2188, B:K.2190, B:T.2191, 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.14: 17 residues within 4Å: Chain C: L.1657, D.1658, F.1663, P.1686, G.1687, A.1688, G.1689, K.1690, S.1691, T.1692, S.1829, Y.1830, S.1833, R.2100, R.2140, R.2143 Ligands: MG.13 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:D.1658, C:D.1658, C:G.1687, C:G.1689, C:K.1690, C:S.1691, C:S.1691, C:T.1692, C:T.1692, C:S.1829, C:S.1833, C:R.2100 Salt bridges: C:R.2140, C:R.2143, C:R.2143

9 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: S.2164, E.2584, R.2627 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.2164 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: 4 residues within 4Å: Chain A: G.2869, G.2870, K.3090 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: Q.2897 Ligands: ADP.12 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: T.2191, D.2629, R.2669 Ligands: ATP.9 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain B: T.2545, D.2605, R.2742 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.2545 MG.13: 3 residues within 4Å: Chain C: S.1691, R.2140 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.1691 MG.15: 3 residues within 4Å: Chain C: T.2017, D.2080 Ligands: ADP.17 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.2017 MG.16: 4 residues within 4Å: Chain C: G.2362, G.2363, K.2576 Ligands: ADP.18 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zimmermann, N. et al., ATP-induced conformational change of axonemal outer dynein arms revealed by cryo-electron tomography. Embo J. (2023)

Release Date

2023-05-10

Peptides

Dynein heavy chain, outer arm protein: A
Outer arm dynein beta heavy chain: B
Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative: 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

Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative

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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