SMTL ID : 7moq.1

The structure of the Tetrahymena thermophila outer dynein arm on doublet microtubule

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-2-2-1-1-1-1-1-1-1-1-1-1-1-6-6-1-2-1-1-mer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)

ADP.1: 15 residues within 4Å: Chain C: A.1871, G.1872, P.1873, A.1874, G.1875, T.1876, G.1877, K.1878, E.1925, N.1977, P.1978, G.1979, Y.1980, R.1983, M.1999 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:A.1871, C:G.1875, C:T.1876, C:G.1877, C:K.1878, C:K.1878, C:N.1977, C:G.1979, C:M.1999 Salt bridges: C:R.1983, C:R.1983 ADP.3: 15 residues within 4Å: Chain C: L.2849, I.2852, G.2869, G.2872, K.2873, Q.2874, S.2875, L.2876, T.2877, R.2878, L.2879, A.2880, G.2881, D.2926, C.3000 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.2872, C:S.2875, C:L.2876, C:R.2878, C:L.2879, C:A.2880, C:G.2881, C:D.2926

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Covalent)

ATP.2: 12 residues within 4Å: Chain C: K.2189, T.2526, S.2527, P.2528, F.2566, N.2568, I.2574, T.2575, E.2577, L.2578, V.2579, Q.2581 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.2527, C:N.2568, C:E.2577

6 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.4: 19 residues within 4Å: Chain Q: G.10, Q.11, C.12, Q.15, I.16, E.69, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, L.225, N.226 Chain S: L.248, E.254 12 PLIP interactions: 12 interactions with chain Q Hydrogen bonds: Q:Q.11, Q:C.12, Q:S.138, Q:G.141, Q:T.143, Q:G.144, Q:D.177, Q:E.181, Q:N.204, Q:N.226, Q:N.226, Q:N.226 GDP.9: 19 residues within 4Å: Chain U: G.10, Q.11, C.12, Q.15, I.16, E.69, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, L.225, N.226 Chain W: L.248, E.254 12 PLIP interactions: 12 interactions with chain U Hydrogen bonds: U:Q.11, U:C.12, U:S.138, U:G.141, U:T.143, U:G.144, U:D.177, U:E.181, U:N.204, U:N.226, U:N.226, U:N.226 GDP.12: 17 residues within 4Å: Chain Y: G.10, Q.11, C.12, Q.15, I.16, E.69, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, L.225, N.226 12 PLIP interactions: 12 interactions with chain Y Hydrogen bonds: Y:Q.11, Y:C.12, Y:S.138, Y:G.141, Y:T.143, Y:G.144, Y:D.177, Y:E.181, Y:N.204, Y:N.226, Y:N.226, Y:N.226 GDP.15: 19 residues within 4Å: Chain 3: G.10, Q.11, C.12, Q.15, I.16, E.69, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, L.225, N.226 Chain 6: L.248, E.254 12 PLIP interactions: 12 interactions with chain 3 Hydrogen bonds: 3:Q.11, 3:C.12, 3:S.138, 3:G.141, 3:T.143, 3:G.144, 3:D.177, 3:E.181, 3:N.204, 3:N.226, 3:N.226, 3:N.226 GDP.18: 19 residues within 4Å: Chain 2: L.248, E.254 Chain 5: G.10, Q.11, C.12, Q.15, I.16, E.69, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, L.225, N.226 12 PLIP interactions: 12 interactions with chain 5 Hydrogen bonds: 5:Q.11, 5:C.12, 5:S.138, 5:G.141, 5:T.143, 5:G.144, 5:D.177, 5:E.181, 5:N.204, 5:N.226, 5:N.226, 5:N.226 GDP.21: 17 residues within 4Å: Chain 7: G.10, Q.11, C.12, Q.15, I.16, E.69, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, L.225, N.226 12 PLIP interactions: 12 interactions with chain 7 Hydrogen bonds: 7:Q.11, 7:C.12, 7:S.138, 7:G.141, 7:T.143, 7:G.144, 7:D.177, 7:E.181, 7:N.204, 7:N.226, 7:N.226, 7:N.226

6 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.5: 27 residues within 4Å: Chain Q: L.246, N.247, K.252 Chain R: G.10, Q.11, G.12, Q.15, V.16, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, T.179, E.183, N.206, Y.224, N.228, I.231 Ligands: MG.6 19 PLIP interactions: 17 interactions with chain R, 2 interactions with chain Q Hydrogen bonds: R:Q.11, R:Q.11, R:G.12, R:A.99, R:N.101, R:N.101, R:S.140, R:G.143, R:G.144, R:T.145, R:G.146, R:T.179, R:E.183, R:N.206, R:N.228, R:N.228, R:N.228 Salt bridges: Q:K.252, Q:K.252 GTP.7: 27 residues within 4Å: Chain S: G.10, Q.11, G.12, Q.15, V.16, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, T.179, E.183, N.206, Y.224, N.228, I.231 Chain U: L.246, N.247, K.252 Ligands: MG.8 19 PLIP interactions: 17 interactions with chain S, 2 interactions with chain U Hydrogen bonds: S:Q.11, S:Q.11, S:G.12, S:A.99, S:N.101, S:N.101, S:S.140, S:G.143, S:G.144, S:T.145, S:G.146, S:T.179, S:E.183, S:N.206, S:N.228, S:N.228, S:N.228 Salt bridges: U:K.252, U:K.252 GTP.10: 27 residues within 4Å: Chain W: G.10, Q.11, G.12, Q.15, V.16, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, T.179, E.183, N.206, Y.224, N.228, I.231 Chain Y: L.246, N.247, K.252 Ligands: MG.11 19 PLIP interactions: 17 interactions with chain W, 2 interactions with chain Y Hydrogen bonds: W:Q.11, W:Q.11, W:G.12, W:A.99, W:N.101, W:N.101, W:S.140, W:G.143, W:G.144, W:T.145, W:G.146, W:T.179, W:E.183, W:N.206, W:N.228, W:N.228, W:N.228 Salt bridges: Y:K.252, Y:K.252 GTP.13: 27 residues within 4Å: Chain 2: G.10, Q.11, G.12, Q.15, V.16, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, T.179, E.183, N.206, Y.224, N.228, I.231 Chain 3: L.246, N.247, K.252 Ligands: MG.14 19 PLIP interactions: 17 interactions with chain 2, 2 interactions with chain 3 Hydrogen bonds: 2:Q.11, 2:Q.11, 2:G.12, 2:A.99, 2:N.101, 2:N.101, 2:S.140, 2:G.143, 2:G.144, 2:T.145, 2:G.146, 2:T.179, 2:E.183, 2:N.206, 2:N.228, 2:N.228, 2:N.228 Salt bridges: 3:K.252, 3:K.252 GTP.16: 27 residues within 4Å: Chain 4: G.10, Q.11, G.12, Q.15, V.16, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, T.179, E.183, N.206, Y.224, N.228, I.231 Chain 5: L.246, N.247, K.252 Ligands: MG.17 19 PLIP interactions: 17 interactions with chain 4, 2 interactions with chain 5 Hydrogen bonds: 4:Q.11, 4:Q.11, 4:G.12, 4:A.99, 4:N.101, 4:N.101, 4:S.140, 4:G.143, 4:G.144, 4:T.145, 4:G.146, 4:T.179, 4:E.183, 4:N.206, 4:N.228, 4:N.228, 4:N.228 Salt bridges: 5:K.252, 5:K.252 GTP.19: 27 residues within 4Å: Chain 6: G.10, Q.11, G.12, Q.15, V.16, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, T.179, E.183, N.206, Y.224, N.228, I.231 Chain 7: L.246, N.247, K.252 Ligands: MG.20 19 PLIP interactions: 17 interactions with chain 6, 2 interactions with chain 7 Hydrogen bonds: 6:Q.11, 6:Q.11, 6:G.12, 6:A.99, 6:N.101, 6:N.101, 6:S.140, 6:G.143, 6:G.144, 6:T.145, 6:G.146, 6:T.179, 6:E.183, 6:N.206, 6:N.228, 6:N.228, 6:N.228 Salt bridges: 7:K.252, 7:K.252

6 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain R: D.69, E.71, T.145 Ligands: GTP.5 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:E.71 MG.8: 4 residues within 4Å: Chain S: D.69, E.71, T.145 Ligands: GTP.7 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:E.71 MG.11: 4 residues within 4Å: Chain W: D.69, E.71, T.145 Ligands: GTP.10 1 PLIP interactions: 1 interactions with chain W Metal complexes: W:E.71 MG.14: 4 residues within 4Å: Chain 2: D.69, E.71, T.145 Ligands: GTP.13 1 PLIP interactions: 1 interactions with chain 2 Metal complexes: 2:E.71 MG.17: 4 residues within 4Å: Chain 4: D.69, E.71, T.145 Ligands: GTP.16 1 PLIP interactions: 1 interactions with chain 4 Metal complexes: 4:E.71 MG.20: 4 residues within 4Å: Chain 6: D.69, E.71, T.145 Ligands: GTP.19 1 PLIP interactions: 1 interactions with chain 6 Metal complexes: 6:E.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kubo, S. et al., Remodeling and activation mechanisms of outer arm dyneins revealed by cryo-EM. Embo Rep. (2021)

Release Date

2021-07-14

Peptides

Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative: A
Outer arm dynein beta heavy chain: B
Dynein heavy chain, outer arm protein: C
Dynein intermediate chain 2: D0
Flagellar outer dynein arm intermediate protein, putative: E1
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 2A: N
Dynein light chain tctex-type 1 protein: O
Thioredoxin: P
Tubulin beta chain: QUY357
Tubulin alpha chain: RSW246
Outer dynein arm docking complex protein oda protein: T
Docking complex 1/2 protein: V8
Docking complex 1 protein: X
Outer dynein arm docking complex protein oda protein: Z

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

0
d

E
E

1
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

U
U

Y
Y

3
u

5
q

7
y

R
R

S
S

W
W

2
s

4
r

6
w

T
T

V
V

8
x

X
X

Z
Z

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

Outer arm dynein beta heavy chain

Dynein heavy chain, outer arm protein

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 2A

Dynein light chain tctex-type 1 protein

Thioredoxin

Tubulin beta chain

Tubulin alpha chain

Outer dynein arm docking complex protein oda protein

Docking complex 1/2 protein

Docking complex 1 protein

Outer dynein arm docking complex protein oda protein

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