SMTL ID : 6f38.1

Cryo-EM structure of two dynein tail domains bound to dynactin and HOOK3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 12 residues within 4Å: Chain A: N.16, G.17, V.20, S.160, G.161, D.162, K.218, E.219, G.302, G.303, S.304, L.306 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.162, A:D.162, A:E.219, A:G.303 ADP.2: 11 residues within 4Å: Chain B: G.17, S.18, G.19, V.20, S.160, G.161, D.162, E.219, G.303, S.304, L.306 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.18, B:G.19, B:V.20, B:V.20, B:S.160, B:G.161 ADP.3: 14 residues within 4Å: Chain C: N.16, G.17, S.18, G.19, V.20, S.160, G.161, D.162, G.187, E.219, G.302, G.303, S.304, L.306 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:N.16, C:S.18, C:G.19, C:V.20, C:V.20, C:G.161, C:E.219, C:G.303, C:S.304 ADP.4: 13 residues within 4Å: Chain D: G.17, S.18, G.19, V.20, S.160, G.161, D.162, G.187, E.219, G.302, G.303, S.304, L.306 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.18, D:G.19, D:V.20, D:V.20, D:D.162, D:G.187, D:E.219, D:G.303, D:S.304 ADP.5: 13 residues within 4Å: Chain E: N.16, G.17, S.18, G.19, V.20, S.160, G.161, D.162, E.219, G.302, G.303, S.304, L.306 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:S.18, E:G.19, E:V.20, E:V.20, E:E.219, E:G.303, E:S.304 ADP.6: 11 residues within 4Å: Chain F: G.17, S.18, G.19, V.20, S.160, G.161, D.162, E.219, G.303, S.304, L.306 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:G.17, F:S.18, F:G.19, F:V.20, F:G.303, F:S.304 ADP.7: 11 residues within 4Å: Chain G: G.17, S.18, G.19, V.20, S.160, G.161, D.162, 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:V.20, G:G.302, G:G.303, G:L.306 ADP.9: 11 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 6 PLIP interactions: 6 interactions with chain I Hydrogen bonds: I:S.18, I:G.19, I:V.20, I:V.20, I:D.162, I:G.303 ADP.10: 10 residues within 4Å: Chain J: G.21, E.22, A.23, F.24, Y.143, C.215, G.308, T.309, M.311, L.312 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:G.21, J:A.23, J:F.24, J:M.311

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

ATP.8: 12 residues within 4Å: Chain H: N.12, G.13, S.14, G.15, M.16, G.156, D.157, G.182, E.214, G.302, T.303, M.305 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:S.14, H:G.15, H:M.16, H:G.156, H:D.157, H:G.302

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Urnavicius, L. et al., Cryo-EM shows how dynactin recruits two dyneins for faster movement. Nature (2018)

Release Date

2018-01-17

Peptides

ARP1 actin related protein 1 homolog A: ABCDEFGI
Actin, cytoplasmic 1: H
Actin related protein 10 homolog: J
Capping protein (Actin filament) muscle Z-line, alpha 1: K
F-actin capping protein beta subunit: L
Dynactin Subunit 2: M
Dynactin Subunit 2: N
Dynactin Subunit 3: OP
Dynactin Subunit 2: QR
Dynactin 6: S
Dynactin subunit 5: T
HOOK3: Uh
Dynactin Subunit 4: V
Dynactin Subunit 1: W
Dynactin subunit 2: X
Dynactin subunit 2: Y
Dynactin subunit 2: Z
Dynactin subunit 2: 0
Cytoplasmic dynein 1 heavy chain 1: 129a
Cytoplasmic dynein 1 intermediate chain 2: 34bc
Cytoplasmic dynein 1 light intermediate chain 2: 56de
Dynein light chain roadblock-type 1: 78fg
Dynactin Subunit 1: i

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

O
O

P
P

Q
Q

R
R

S
U

T
V

U
X

h
x

V
Y

W
Z

X
a

Y
b

Z
c

0
d

1
e

2
f

9
m

a
n

3
g

4
h

b
o

c
p

5
i

6
j

d
q

e
r

7
k

8
l

f
s

g
t

i
z

ARP1 actin related protein 1 homolog A

Actin, cytoplasmic 1

Actin related protein 10 homolog

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

F-actin capping protein beta subunit

Dynactin Subunit 2

Dynactin Subunit 2

Dynactin Subunit 3

Dynactin Subunit 2

Dynactin 6

Dynactin subunit 5

HOOK3

Dynactin Subunit 4

Dynactin Subunit 1

Dynactin subunit 2

Dynactin subunit 2

Dynactin subunit 2

Dynactin subunit 2

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

Dynactin Subunit 1

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