SMTL ID : 8ptk.1

Composite structure of Dynein-Dynactin-JIP3-LIS1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 11 residues within 4Å: Chain E: G.17, S.18, G.19, V.20, G.161, D.162, K.218, E.219, G.303, S.304, L.306 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:N.16, E:S.18, E:G.19, E:V.20, E:D.162 ADP.2: 13 residues within 4Å: Chain F: G.17, S.18, G.19, V.20, G.161, D.162, K.218, E.219, G.302, G.303, S.304, L.306, L.337 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:S.18, F:G.19, F:V.20, F:V.20, F:D.162, F:L.306 ADP.3: 12 residues within 4Å: Chain G: G.17, S.18, G.19, V.20, G.161, D.162, K.218, E.219, G.302, G.303, S.304, L.306 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:S.18, G:G.19, G:V.20, G:V.20, G:D.162, G:G.303, G:L.306, G:L.337 ADP.4: 14 residues within 4Å: Chain H: 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 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:S.18, H:G.19, H:V.20, H:D.162, H:G.163, H:G.187, H:E.219, H:G.303 ADP.5: 12 residues within 4Å: Chain I: G.17, S.18, G.19, V.20, G.161, D.162, K.218, E.219, G.303, S.304, L.306, L.337 6 PLIP interactions: 6 interactions with chain I Hydrogen bonds: I:S.18, I:V.20, I:D.162, I:E.219, I:G.303, I:L.337 ADP.6: 11 residues within 4Å: Chain J: G.17, S.18, G.19, V.20, G.161, D.162, K.218, E.219, G.303, S.304, L.306 6 PLIP interactions: 6 interactions with chain J Hydrogen bonds: J:S.18, J:G.19, J:V.20, J:V.20, J:D.162, J:E.219 ADP.7: 10 residues within 4Å: Chain K: G.17, S.18, G.161, D.162, K.218, E.219, G.302, G.303, S.304, L.306 5 PLIP interactions: 5 interactions with chain K Hydrogen bonds: K:S.18, K:V.20, K:D.162, K:E.219, K:G.303 ADP.9: 12 residues within 4Å: Chain M: G.17, S.18, V.20, G.161, D.162, K.218, E.219, G.302, G.303, S.304, L.306, L.337 5 PLIP interactions: 5 interactions with chain M Hydrogen bonds: M:S.18, M:D.162, M:G.303, M:L.306, M:L.337 ADP.14: 8 residues within 4Å: Chain 5: V.1880, A.1908, G.1909, T.1910, G.1911, K.1912, T.1913 Ligands: MG.15 7 PLIP interactions: 7 interactions with chain 5 Hydrogen bonds: 5:V.1880, 5:V.1880, 5:G.1909, 5:T.1910, 5:G.1911, 5:K.1912, 5:T.1913 ADP.18: 8 residues within 4Å: Chain 5: V.2567, V.2568, V.2569, P.2597, G.2598, K.2601, T.2602, P.2796 7 PLIP interactions: 7 interactions with chain 5 Hydrogen bonds: 5:V.2569, 5:V.2569, 5:G.2598, 5:K.2601, 5:K.2601, 5:T.2602, 5:M.2603 ADP.19: 12 residues within 4Å: Chain 5: P.2908, L.2909, V.2910, V.2938, S.2939, G.2940, A.2941, G.2942, K.2943, T.2944, T.2945, N.3650 9 PLIP interactions: 9 interactions with chain 5 Hydrogen bonds: 5:V.2910, 5:V.2910, 5:G.2940, 5:A.2941, 5:G.2942, 5:K.2943, 5:T.2944, 5:T.2945, 5:N.3650 ADP.20: 10 residues within 4Å: Chain 6: L.1879, V.1880, A.1908, G.1909, T.1910, G.1911, K.1912, T.1913, E.1914 Ligands: MG.21 7 PLIP interactions: 7 interactions with chain 6 Hydrogen bonds: 6:V.1880, 6:V.1880, 6:G.1909, 6:T.1910, 6:G.1911, 6:K.1912, 6:T.1913 ADP.24: 8 residues within 4Å: Chain 6: V.2567, V.2568, V.2569, G.2598, K.2601, T.2602, I.2747, P.2796 7 PLIP interactions: 7 interactions with chain 6 Hydrogen bonds: 6:V.2569, 6:V.2569, 6:G.2598, 6:K.2601, 6:K.2601, 6:T.2602, 6:M.2603 ADP.25: 12 residues within 4Å: Chain 6: P.2908, L.2909, V.2910, V.2938, S.2939, G.2940, A.2941, G.2942, K.2943, T.2944, T.2945, N.3650 9 PLIP interactions: 9 interactions with chain 6 Hydrogen bonds: 6:V.2910, 6:V.2910, 6:G.2940, 6:A.2941, 6:G.2942, 6:K.2943, 6:T.2944, 6:T.2945, 6:N.3650 ADP.26: 10 residues within 4Å: Chain d: L.1879, V.1880, A.1908, G.1909, T.1910, G.1911, K.1912, T.1913, E.1914, L.2090 8 PLIP interactions: 8 interactions with chain d Hydrogen bonds: d:V.1880, d:V.1880, d:G.1909, d:T.1910, d:G.1911, d:K.1912, d:T.1913, d:E.1914 ADP.31: 10 residues within 4Å: Chain e: L.1879, V.1880, A.1908, G.1909, T.1910, G.1911, K.1912, T.1913, E.1914, L.2090 9 PLIP interactions: 9 interactions with chain e Hydrogen bonds: e:V.1880, e:V.1880, e:P.1907, e:G.1909, e:T.1910, e:G.1911, e:K.1912, e:T.1913, e:E.1914

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

ATP.8: 14 residues within 4Å: Chain L: G.13, S.14, G.15, M.16, S.155, G.156, D.157, G.158, K.213, E.214, G.301, G.302, T.303, M.305 7 PLIP interactions: 7 interactions with chain L Hydrogen bonds: L:S.14, L:G.15, L:M.16, L:D.157, L:G.158, L:G.302, L:M.305 ATP.10: 12 residues within 4Å: Chain N: G.21, E.22, A.23, F.24, C.141, G.142, Y.143, R.144, G.307, G.308, T.309, M.311 8 PLIP interactions: 8 interactions with chain N Hydrogen bonds: N:E.22, N:A.23, N:F.24, N:F.24, N:Y.143, N:R.144, N:G.308, N:T.309 ATP.16: 10 residues within 4Å: Chain 5: T.2192, S.2226, G.2227, S.2228, G.2229, K.2230, S.2231, M.2232, N.2377 Ligands: MG.17 7 PLIP interactions: 7 interactions with chain 5 Hydrogen bonds: 5:T.2192, 5:G.2227, 5:S.2228, 5:G.2229, 5:K.2230, 5:S.2231, 5:M.2232 ATP.22: 11 residues within 4Å: Chain 6: L.2191, T.2192, S.2226, G.2227, S.2228, G.2229, K.2230, S.2231, M.2232, N.2377 Ligands: MG.23 7 PLIP interactions: 7 interactions with chain 6 Hydrogen bonds: 6:T.2192, 6:G.2227, 6:S.2228, 6:G.2229, 6:K.2230, 6:S.2231, 6:M.2232 ATP.27: 14 residues within 4Å: Ligands: MG.28 Chain d: L.2191, T.2192, P.2225, S.2226, G.2227, S.2228, G.2229, K.2230, S.2231, M.2232, M.2373, N.2377, R.2726 9 PLIP interactions: 9 interactions with chain d Hydrogen bonds: d:T.2192, d:T.2192, d:P.2225, d:G.2227, d:S.2228, d:G.2229, d:K.2230, d:S.2231, d:M.2232 ATP.32: 13 residues within 4Å: Ligands: MG.33 Chain e: L.2191, T.2192, S.2226, G.2227, S.2228, G.2229, K.2230, S.2231, M.2232, M.2373, N.2377, R.2726 8 PLIP interactions: 8 interactions with chain e Hydrogen bonds: e:T.2192, e:T.2192, e:G.2227, e:S.2228, e:G.2229, e:K.2230, e:S.2231, e:M.2232

3 x ZN: ZINC ION(Non-covalent)

ZN.11: 4 residues within 4Å: Chain 1: C.30, C.33, C.284, C.287 No protein-ligand interaction detected (PLIP) ZN.12: 4 residues within 4Å: Chain 1: C.51, C.54, C.70, C.73 No protein-ligand interaction detected (PLIP) ZN.13: 5 residues within 4Å: Chain 1: C.76, C.79, H.81, C.111, C.114 No protein-ligand interaction detected (PLIP)

6 x MG: MAGNESIUM ION(Non-covalent)

MG.15: 2 residues within 4Å: Chain 5: T.1913 Ligands: ADP.14 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain 5: S.2231 Ligands: ATP.16 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain 6: T.1913 Ligands: ADP.20 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain 6: S.2231 Ligands: ATP.22 No protein-ligand interaction detected (PLIP) MG.28: 2 residues within 4Å: Ligands: ATP.27 Chain d: S.2231 No protein-ligand interaction detected (PLIP) MG.33: 2 residues within 4Å: Ligands: ATP.32 Chain e: S.2231 No protein-ligand interaction detected (PLIP)

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

ANP.29: 11 residues within 4Å: Chain d: V.2569, P.2596, P.2597, G.2598, S.2599, G.2600, K.2601, T.2602, M.2603, P.2796, T.2800 9 PLIP interactions: 9 interactions with chain d Hydrogen bonds: d:V.2569, d:V.2569, d:P.2596, d:G.2598, d:S.2599, d:G.2600, d:K.2601, d:T.2602, d:M.2603 ANP.30: 9 residues within 4Å: Chain d: P.2908, L.2909, V.2910, S.2939, G.2940, A.2941, G.2942, K.2943, T.2944 6 PLIP interactions: 6 interactions with chain d Hydrogen bonds: d:V.2910, d:V.2910, d:G.2940, d:A.2941, d:G.2942, d:K.2943 ANP.34: 10 residues within 4Å: Chain e: V.2569, P.2596, P.2597, G.2598, S.2599, G.2600, K.2601, T.2602, M.2603, T.2800 8 PLIP interactions: 8 interactions with chain e Hydrogen bonds: e:V.2569, e:V.2569, e:G.2598, e:S.2599, e:G.2600, e:K.2601, e:T.2602, e:M.2603 ANP.35: 9 residues within 4Å: Chain e: P.2908, L.2909, V.2910, S.2939, G.2940, A.2941, G.2942, K.2943, T.2944 6 PLIP interactions: 6 interactions with chain e Hydrogen bonds: e:V.2910, e:V.2910, e:G.2940, e:A.2941, e:G.2942, e:K.2943

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, K. et al., Molecular mechanism of dynein-dynactin complex assembly by LIS1. Science (2024)

Release Date

2024-03-27

Peptides

Platelet-activating factor acetylhydrolase IB subunit beta: ABCD
ARP1 actin related protein 1 homolog A: EFGHIJKM
Actin, cytoplasmic 1: L
Arp11: N
Capping protein (Actin filament) muscle Z-line, alpha 1: O
F-actin-capping protein subunit beta: P
Dynactin subunit 2: QRTU
Dynactin subunit 3: SV
Dynactin subunit 1: WX
Dynactin 6: Y
Dynactin subunit 5: Z
C-Jun-amino-terminal kinase-interacting protein 3: 0o
Dynactin subunit 4: 1
Dynein light chain 1, cytoplasmic: 2349
Cytoplasmic dynein 1 heavy chain 1: 56de
Cytoplasmic dynein 1 intermediate chain 2: 78fg
Cytoplasmic dynein 1 light intermediate chain 2: ahil
Dynein light chain Tctex-type 1: bcmp
Dynein light chain roadblock-type 1: jknq

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
A

F
B

G
C

H
D

I
E

J
F

K
G

M
I

L
H

N
J

O
K

P
L

Q
M

R
N

T
P

U
Q

S
O

V
R

W
S

X
T

Y
U

Z
W

0
X

o
x

1
Y

2
a

3
b

4
d

9
i

5
e

6
f

d
m

e
n

7
g

8
h

f
o

g
p

a
j

h
q

i
r

l
u

b
k

c
l

m
v

p
y

j
s

k
t

n
w

q
z

Platelet-activating factor acetylhydrolase IB subunit beta

ARP1 actin related protein 1 homolog A

Actin, cytoplasmic 1

Arp11

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

F-actin-capping protein subunit beta

Dynactin subunit 2

Dynactin subunit 3

Dynactin subunit 1

Dynactin 6

Dynactin subunit 5

C-Jun-amino-terminal kinase-interacting protein 3

Dynactin subunit 4

Dynein light chain 1, cytoplasmic

Cytoplasmic dynein 1 heavy chain 1

Cytoplasmic dynein 1 intermediate chain 2

Cytoplasmic dynein 1 light intermediate chain 2

Dynein light chain Tctex-type 1

Dynein light chain roadblock-type 1

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