SMTL ID : 9dgu.1

structure of dynactin, dynein tail with two BICDR from dynein-dynactin-BICDR on microtubules

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 12 residues within 4Å: Chain A: G.17, S.18, G.19, V.20, S.160, G.161, D.162, G.187, E.219, G.303, S.304, L.306 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.18, A:G.19, A:V.20, A:D.162, A:E.219 ADP.2: 11 residues within 4Å: Chain B: G.17, S.18, G.19, V.20, G.161, D.162, E.219, G.302, 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:D.162, B:E.219 ADP.3: 13 residues within 4Å: Chain C: G.17, S.18, G.19, S.160, G.161, D.162, G.187, E.219, G.302, G.303, S.304, L.306, F.307 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.18, C:G.19, C:V.20, C:D.162, C:E.219, C:G.303, C:S.304 ADP.4: 12 residues within 4Å: Chain D: G.17, S.18, G.19, V.20, G.161, D.162, G.163, E.219, G.302, G.303, S.304, L.306 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.18, D:G.19, D:V.20, D:D.162, D:G.163, D:G.303, D:L.306 ADP.5: 10 residues within 4Å: Chain E: G.17, S.18, G.19, V.20, G.161, D.162, G.303, S.304, L.306, F.307 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:S.18, E:G.19, E:V.20, E:V.20, E:D.162, E:L.306 ADP.6: 13 residues within 4Å: Chain F: G.17, S.18, G.19, V.20, G.161, D.162, G.187, E.219, G.302, G.303, S.304, L.306, F.307 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:S.18, F:G.19, F:V.20, F:V.20, F:D.162, F:G.303, F:L.306 ADP.7: 14 residues within 4Å: Chain G: 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, F.307 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:S.18, G:G.19, G:D.162, G:E.219, G:G.303, G:S.304 ADP.9: 13 residues within 4Å: Chain I: G.17, S.18, G.19, V.20, G.161, D.162, G.187, R.188, E.219, G.302, 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:D.162, I:G.303, I:S.304 ADP.10: 13 residues within 4Å: Chain J: G.21, E.22, A.23, F.24, C.141, G.142, Y.143, G.168, G.307, G.308, T.309, M.311, L.312 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:E.22, J:A.23, J:F.24, J:Y.143, J:G.308

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

ATP.8: 13 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, M.305 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:S.14, H:G.15, H:M.16, H:D.157, H:E.214, H:G.302

3 x ZN: ZINC ION(Non-covalent)

ZN.11: 4 residues within 4Å: Chain V: C.30, C.33, Q.286, C.287 No protein-ligand interaction detected (PLIP) ZN.12: 3 residues within 4Å: Chain V: C.51, C.70, C.73 No protein-ligand interaction detected (PLIP) ZN.13: 6 residues within 4Å: Chain V: C.76, C.79, M.80, H.81, C.111, C.114 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rao, Q. et al., Structure of dynein-dynactin on microtubules. To Be Published

Release Date

2025-09-10

Peptides

Alpha-centractin: ABCDEFGI
Actin, cytoplasmic 1: H
Actin-related protein 10: J
F-actin-capping protein subunit alpha-1: K
F-actin-capping protein subunit beta: L
Dynactin subunit 2: MNPQ
Dynactin subunit 3: OR
Dynactin subunit 6: S
Dynactin subunit 5: T
Dynactin subunit 1: UW
Dynactin subunit 4: V
BICD family-like cargo adapter 1: XYZ0
Cytoplasmic dynein 1 heavy chain 1: 1267
Cytoplasmic dynein 1 intermediate chain 2: 3489
Dynein light intermediate chain: 5a

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
U

T
V

U
W

W
Z

V
Y

X
a

Y
b

Z
c

0
d

1
e

2
f

6
m

7
n

3
g

4
h

8
o

9
p

5
j

a
q

Alpha-centractin

Actin, cytoplasmic 1

Actin-related protein 10

F-actin-capping protein subunit alpha-1

F-actin-capping protein subunit beta

Dynactin subunit 2

Dynactin subunit 3

Dynactin subunit 6

Dynactin subunit 5

Dynactin subunit 1

Dynactin subunit 4

BICD family-like cargo adapter 1

Cytoplasmic dynein 1 heavy chain 1

Cytoplasmic dynein 1 intermediate chain 2

Dynein light intermediate chain

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