SMTL ID : 6f1t.1

Cryo-EM structure of two dynein tail domains bound to dynactin and BICDR1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: D.15, G.17, S.18, V.20, K.22, Q.142, S.160, G.161, D.162, G.187, K.218, E.219, G.302, G.303, S.304, L.306, F.307 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.18, A:Q.142, A:Q.142, A:D.162, A:D.162, A:K.218, A:E.219, A:G.303 Salt bridges: A:K.22, A:K.22 pi-Stacking: A:F.307 ADP.2: 15 residues within 4Å: Chain B: N.16, G.17, S.18, G.19, V.20, K.22, G.161, D.162, K.215, K.218, E.219, G.303, S.304, L.306, F.307 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.16, B:S.18, B:G.19, B:V.20, B:D.162, B:D.162, B:K.218, B:E.219, B:G.303 Salt bridges: B:K.22, B:K.22 pi-Stacking: B:F.307 ADP.3: 15 residues within 4Å: Chain C: N.16, G.17, S.18, G.19, V.20, K.22, G.161, D.162, K.218, E.219, G.303, S.304, L.306, F.307, L.337 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.18, C:G.19, C:V.20, C:V.20, C:D.162, C:D.162, C:D.162, C:K.218, C:E.219, C:G.303 Salt bridges: C:K.22, C:K.22 pi-Stacking: C:F.307 ADP.4: 16 residues within 4Å: Chain D: G.17, S.18, G.19, V.20, K.22, S.160, G.161, D.162, K.218, E.219, G.302, G.303, S.304, L.306, F.307, L.337 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:S.18, D:G.19, D:V.20, D:D.162, D:D.162, D:D.162, D:K.218, D:G.303, D:S.304 Salt bridges: D:K.22, D:K.22 ADP.5: 16 residues within 4Å: Chain E: G.17, S.18, G.19, V.20, K.22, G.161, D.162, G.187, K.215, K.218, E.219, G.302, G.303, S.304, L.306, F.307 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:S.18, E:G.19, E:V.20, E:D.162, E:D.162, E:K.215, E:K.218, E:E.219, E:G.303 Salt bridges: E:K.22, E:K.22 ADP.6: 16 residues within 4Å: Chain F: G.17, V.20, K.22, S.160, G.161, D.162, G.187, K.215, K.218, E.219, G.302, G.303, S.304, L.306, F.307, L.337 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:S.18, F:D.162, F:D.162, F:D.162, F:K.215, F:G.303, F:S.304, F:L.306 Salt bridges: F:K.22, F:K.22 pi-Stacking: F:F.307 ADP.7: 16 residues within 4Å: Chain G: G.17, S.18, G.19, V.20, K.22, G.161, D.162, K.215, K.218, E.219, G.302, G.303, S.304, L.306, F.307, L.337 13 PLIP interactions: 13 interactions with chain G Hydrogen bonds: G:S.18, G:G.19, G:V.20, G:D.162, G:K.215, G:K.215, G:K.218, G:E.219, G:G.303, G:L.306 Salt bridges: G:K.22, G:K.22 pi-Stacking: G:F.307 ADP.9: 16 residues within 4Å: Chain I: G.17, S.18, G.19, V.20, K.22, G.161, D.162, K.215, K.218, E.219, G.302, G.303, S.304, L.306, F.307, L.337 11 PLIP interactions: 11 interactions with chain I Hydrogen bonds: I:S.18, I:G.19, I:V.20, I:V.20, I:D.162, I:K.215, I:K.215, I:K.218, I:E.219, I:G.303 Salt bridges: I:K.22 ADP.10: 14 residues within 4Å: Chain J: L.20, G.21, E.22, A.23, F.24, K.26, G.142, Y.143, K.211, V.212, G.308, T.309, M.311, N.351 7 PLIP interactions: 7 interactions with chain J Hydrogen bonds: J:E.22, J:A.23, J:F.24, J:Y.143, J:G.308 Salt bridges: J:K.26, J:K.26

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

ATP.8: 17 residues within 4Å: Chain H: D.11, G.13, S.14, G.15, M.16, K.18, Q.137, G.156, D.157, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:G.15, H:M.16, H:D.157, H:D.157, H:D.157, H:R.210, H:R.210, H:K.213, H:E.214, H:G.302, H:M.305 Salt bridges: H:K.18, H:K.18, H:K.18 pi-Stacking: H:Y.306

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
BICD family-like cargo adapter 1,BICD family-like cargo adapter 1,BICD family-like cargo adapter 1,BICDR-1: U
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,Cytoplasmic dynein 1 heavy chain 1,Cytoplasmic dynein 1 heavy chain 1,Dynein Heavy Chain,Cytoplasmic dynein 1 heavy chain 1,Cytoplasmic dynein 1 heavy chain 1,Cytoplasmic dynein 1 heavy chain 1,Cytoplasmic dynein 1 heavy chain 1,Dynein Heavy Chain,Cytoplasmic dynein 1 heavy chain 1,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
BICD family-like cargo adapter 1,BICD family-like cargo adapter 1,BICD family-like cargo adapter 1: h
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

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

h
x

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

BICD family-like cargo adapter 1,BICD family-like cargo adapter 1,BICD family-like cargo adapter 1,BICDR-1

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 heavy chain 1,Cytoplasmic dynein 1 heavy chain 1,Dynein Heavy Chain,Cytoplasmic dynein 1 heavy chain 1,Cytoplasmic dynein 1 heavy chain 1,Cytoplasmic dynein 1 heavy chain 1,Cytoplasmic dynein 1 heavy chain 1,Dynein Heavy Chain,Cytoplasmic dynein 1 heavy chain 1,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

BICD family-like cargo adapter 1,BICD family-like cargo adapter 1,BICD family-like cargo adapter 1

Dynactin Subunit 1

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