SMTL ID : 7z8f.1

Composite structure of dynein-dynactin-BICDR on microtubules

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-8-1-1-1-1-4-2-2-1-1-4-1-4-4-4-4-mer

Ligands

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

ADP.1: 12 residues within 4Å: Chain A: G.17, S.18, G.19, V.20, G.161, D.162, E.219, G.302, G.303, S.304, L.306 Ligands: MG.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.18, A:G.19, A:V.20, A:V.20, A:D.162, A:G.303, A:L.306 ADP.3: 11 residues within 4Å: Chain B: G.17, S.18, G.19, V.20, G.161, D.162, G.302, G.303, S.304, L.306 Ligands: MG.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.18, B:G.19, B:D.162, B:G.303 ADP.5: 12 residues within 4Å: Chain C: G.17, S.18, G.19, V.20, G.161, D.162, E.219, G.302, G.303, S.304, L.306 Ligands: MG.6 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.18, C:G.19, C:V.20, C:D.162, C:E.219, C:G.303 ADP.7: 13 residues within 4Å: Chain D: G.17, S.18, G.19, V.20, G.161, D.162, E.219, G.302, G.303, S.304, L.306, L.337 Ligands: MG.8 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.18, D:G.19, D:V.20, D:D.162, D:G.303, D:L.337 ADP.9: 12 residues within 4Å: Chain E: G.17, S.18, G.19, V.20, G.161, D.162, E.219, G.302, G.303, S.304, L.306 Ligands: MG.10 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:S.18, E:G.19, E:V.20, E:D.162, E:E.219, E:G.303 ADP.12: 14 residues within 4Å: Chain F: G.17, S.18, G.19, V.20, G.161, D.162, E.219, G.302, G.303, S.304, L.306, F.307, L.337 Ligands: MG.11 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:S.18, F:G.19, F:V.20, F:D.162, F:G.303, F:L.306, F:L.337 ADP.13: 14 residues within 4Å: Chain G: G.17, S.18, G.19, V.20, G.161, D.162, G.163, K.218, E.219, G.302, G.303, S.304, L.306 Ligands: MG.14 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:S.18, G:G.19, G:V.20, G:D.162, G:G.163, G:G.303, G:L.306 ADP.15: 14 residues within 4Å: Chain H: G.13, S.14, G.15, M.16, G.156, D.157, G.182, K.213, E.214, G.301, G.302, T.303, K.336 Ligands: MG.16 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:S.14, H:G.15, H:M.16, H:D.157, H:G.302, H:M.305, H:K.336 ADP.17: 15 residues within 4Å: Chain I: G.17, S.18, G.19, V.20, G.161, D.162, G.163, G.187, K.218, E.219, G.302, G.303, S.304, L.306 Ligands: MG.18 7 PLIP interactions: 7 interactions with chain I Hydrogen bonds: I:S.18, I:G.19, I:V.20, I:D.162, I:G.163, I:G.303, I:L.306 ADP.24: 9 residues within 4Å: Chain Z: L.1879, V.1880, A.1908, G.1909, T.1910, G.1911, K.1912, T.1913, E.1914 8 PLIP interactions: 8 interactions with chain Z Hydrogen bonds: Z:V.1880, Z:V.1880, Z:G.1909, Z:T.1910, Z:G.1911, Z:K.1912, Z:T.1913, Z:E.1914 ADP.29: 8 residues within 4Å: Chain 0: V.1880, A.1908, G.1909, T.1910, G.1911, K.1912, T.1913, E.1914 9 PLIP interactions: 9 interactions with chain 0 Hydrogen bonds: 0:V.1880, 0:V.1880, 0:G.1909, 0:T.1910, 0:G.1911, 0:G.1911, 0:K.1912, 0:T.1913, 0:E.1914 ADP.34: 8 residues within 4Å: Chain 7: V.1880, A.1908, G.1909, T.1910, G.1911, K.1912, T.1913, E.1914 9 PLIP interactions: 9 interactions with chain 7 Hydrogen bonds: 7:V.1880, 7:V.1880, 7:G.1909, 7:T.1910, 7:G.1911, 7:G.1911, 7:K.1912, 7:T.1913, 7:E.1914 ADP.39: 8 residues within 4Å: Chain 8: V.1880, A.1908, G.1909, T.1910, G.1911, K.1912, T.1913, E.1914 10 PLIP interactions: 10 interactions with chain 8 Hydrogen bonds: 8:V.1880, 8:V.1880, 8:G.1909, 8:G.1909, 8:T.1910, 8:G.1911, 8:G.1911, 8:K.1912, 8:T.1913, 8:E.1914

14 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 1 residues within 4Å: Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Ligands: ADP.12 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Ligands: ADP.13 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Ligands: ADP.15 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Ligands: ADP.17 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Ligands: ATP.19 No protein-ligand interaction detected (PLIP) MG.26: 1 residues within 4Å: Ligands: ATP.25 No protein-ligand interaction detected (PLIP) MG.32: 1 residues within 4Å: Ligands: ATP.30 No protein-ligand interaction detected (PLIP) MG.36: 1 residues within 4Å: Ligands: ATP.35 No protein-ligand interaction detected (PLIP) MG.41: 1 residues within 4Å: Ligands: ATP.40 No protein-ligand interaction detected (PLIP)

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

ATP.19: 12 residues within 4Å: Chain J: G.21, E.22, A.23, F.24, G.142, Y.143, R.144, G.307, G.308, T.309, M.311 Ligands: MG.20 8 PLIP interactions: 8 interactions with chain J Hydrogen bonds: J:E.22, J:A.23, J:F.24, J:F.24, J:Y.143, J:R.144, J:G.308, J:T.309 ATP.25: 12 residues within 4Å: Chain Z: L.2191, T.2192, S.2226, G.2227, S.2228, G.2229, K.2230, S.2231, M.2232, M.2373, R.2726 Ligands: MG.26 9 PLIP interactions: 9 interactions with chain Z Hydrogen bonds: Z:T.2192, Z:T.2192, Z:G.2227, Z:S.2228, Z:G.2229, Z:K.2230, Z:S.2231, Z:M.2232, Z:R.2726 ATP.30: 11 residues within 4Å: Chain 0: L.2191, T.2192, S.2226, G.2227, S.2228, G.2229, K.2230, S.2231, M.2232, M.2373 Ligands: MG.32 8 PLIP interactions: 8 interactions with chain 0 Hydrogen bonds: 0:T.2192, 0:T.2192, 0:G.2227, 0:S.2228, 0:G.2229, 0:K.2230, 0:S.2231, 0:M.2232 ATP.35: 11 residues within 4Å: Chain 7: L.2191, T.2192, S.2226, G.2227, S.2228, G.2229, K.2230, S.2231, M.2232, M.2373 Ligands: MG.36 8 PLIP interactions: 8 interactions with chain 7 Hydrogen bonds: 7:T.2192, 7:T.2192, 7:G.2227, 7:S.2228, 7:G.2229, 7:K.2230, 7:S.2231, 7:M.2232 ATP.40: 12 residues within 4Å: Chain 8: T.2192, S.2226, G.2227, S.2228, G.2229, K.2230, S.2231, M.2232, M.2373, I.2374, R.2726 Ligands: MG.41 9 PLIP interactions: 9 interactions with chain 8 Hydrogen bonds: 8:T.2192, 8:T.2192, 8:G.2227, 8:S.2228, 8:G.2229, 8:K.2230, 8:S.2231, 8:M.2232, 8:R.2726

3 x ZN: ZINC ION(Non-covalent)

ZN.21: 1 residues within 4Å: Chain Y: C.287 No protein-ligand interaction detected (PLIP) ZN.22: 2 residues within 4Å: Chain Y: C.54, C.73 No protein-ligand interaction detected (PLIP) ZN.23: 2 residues within 4Å: Chain Y: C.79, C.114 No protein-ligand interaction detected (PLIP)

8 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.27: 7 residues within 4Å: Chain Z: V.2569, G.2598, S.2599, G.2600, K.2601, T.2602, M.2603 8 PLIP interactions: 8 interactions with chain Z Hydrogen bonds: Z:V.2569, Z:V.2569, Z:G.2598, Z:S.2599, Z:G.2600, Z:K.2601, Z:T.2602, Z:M.2603 ANP.28: 8 residues within 4Å: Chain Z: P.2908, L.2909, V.2910, G.2940, G.2942, K.2943, T.2944, T.2945 6 PLIP interactions: 6 interactions with chain Z Hydrogen bonds: Z:V.2910, Z:V.2910, Z:G.2940, Z:G.2942, Z:K.2943, Z:T.2945 ANP.31: 8 residues within 4Å: Chain 0: P.2908, L.2909, V.2910, G.2940, G.2942, K.2943, T.2944, T.2945 5 PLIP interactions: 5 interactions with chain 0 Hydrogen bonds: 0:V.2910, 0:V.2910, 0:G.2940, 0:G.2942, 0:K.2943 ANP.33: 9 residues within 4Å: Chain 0: V.2569, G.2598, S.2599, G.2600, K.2601, T.2602, M.2603, P.2796, R.2797 8 PLIP interactions: 8 interactions with chain 0 Hydrogen bonds: 0:V.2569, 0:V.2569, 0:G.2598, 0:S.2599, 0:G.2600, 0:K.2601, 0:T.2602, 0:M.2603 ANP.37: 8 residues within 4Å: Chain 7: V.2569, G.2598, S.2599, G.2600, K.2601, T.2602, M.2603, R.2797 8 PLIP interactions: 8 interactions with chain 7 Hydrogen bonds: 7:V.2569, 7:V.2569, 7:G.2598, 7:S.2599, 7:G.2600, 7:K.2601, 7:T.2602, 7:M.2603 ANP.38: 8 residues within 4Å: Chain 7: P.2908, L.2909, V.2910, G.2940, G.2942, K.2943, T.2944, T.2945 5 PLIP interactions: 5 interactions with chain 7 Hydrogen bonds: 7:V.2910, 7:V.2910, 7:G.2940, 7:G.2942, 7:K.2943 ANP.42: 10 residues within 4Å: Chain 8: V.2569, P.2597, G.2598, S.2599, G.2600, K.2601, T.2602, M.2603, P.2796, R.2797 8 PLIP interactions: 8 interactions with chain 8 Hydrogen bonds: 8:V.2569, 8:V.2569, 8:G.2598, 8:S.2599, 8:G.2600, 8:K.2601, 8:T.2602, 8:M.2603 ANP.43: 8 residues within 4Å: Chain 8: P.2908, L.2909, V.2910, G.2940, G.2942, K.2943, T.2944, T.2945 5 PLIP interactions: 5 interactions with chain 8 Hydrogen bonds: 8:V.2910, 8:V.2910, 8:G.2940, 8:G.2942, 8:K.2943

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaaban, S. et al., Structure of dynein-dynactin on microtubules shows tandem adaptor binding. Nature (2022)

Release Date

2022-07-27

Peptides

ARP1 actin related protein 1 homolog A: ABCDEFGI
Actin, cytoplasmic 1: H
Arp11: J
Capping protein (Actin filament) muscle Z-line, alpha 1: K
F-actin capping protein beta subunit: L
Dynactin subunit 2: MNPQ
Dynactin subunit 3: OR
Dynactin subunit 1: ST
Dynactin 6: U
Dynactin subunit 5: V
BICD family-like cargo adapter 1: WXfg
Dynactin subunit 4: Y
Cytoplasmic dynein 1 heavy chain 1: Z078
Cytoplasmic dynein 1 intermediate chain 2: 129a
Cytoplasmic dynein 1 light intermediate chain 2: 34bc
Dynein light chain roadblock-type 1: 56de

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

I
I

H
H

J
J

K
K

L
L

M
M

N
N

P
P

Q
Q

O
O

R
R

S
S

T
T

U
U

V
V

W
W

X
X

f
w

g
x

Y
Y

Z
e

0
f

7
m

8
n

1
g

2
h

9
o

a
p

3
i

4
j

b
q

c
r

5
k

6
l

d
s

e
t

ARP1 actin related protein 1 homolog A

Actin, cytoplasmic 1

Arp11

Capping protein (Actin filament) muscle Z-line, alpha 1

F-actin capping protein beta subunit

Dynactin subunit 2

Dynactin subunit 3

Dynactin subunit 1

Dynactin 6

Dynactin subunit 5

BICD family-like cargo adapter 1

Dynactin subunit 4

Cytoplasmic dynein 1 heavy chain 1

Cytoplasmic dynein 1 intermediate chain 2

Cytoplasmic dynein 1 light intermediate chain 2

Dynein light chain roadblock-type 1

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