SMTL ID : 6znl.1

Cryo-EM structure of the dynactin complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: D.15, G.17, S.18, V.20, K.22, Q.142, D.159, 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 A Hydrogen bonds: A:S.18, A:V.20, A:Q.142, A:D.162, A:D.162, A:K.215, A:K.218, A:E.219, A:G.303, A:L.337 Salt bridges: A:K.22, A:K.22 pi-Stacking: A:F.307 ADP.2: 17 residues within 4Å: Chain B: D.15, G.17, G.19, V.20, K.22, Q.142, D.159, G.161, D.162, K.215, K.218, E.219, G.303, S.304, L.306, F.307, L.337 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:D.15, B:G.19, B:V.20, B:Q.142, B:D.162, B:D.162, B:K.215, B:K.218, B:E.219, B:G.303, B:L.337 Salt bridges: B:K.22, B:K.22 pi-Stacking: B:F.307 ADP.3: 18 residues within 4Å: Chain C: D.15, G.17, S.18, G.19, V.20, K.22, Q.142, G.161, D.162, K.215, K.218, E.219, G.302, G.303, S.304, L.306, F.307, L.337 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:S.18, C:G.19, C:V.20, C:V.20, C:Q.142, C:Q.142, C:D.162, C:K.215, C:K.215, C:K.218, C:E.219, C:G.303 Salt bridges: C:K.22, C:K.22 pi-Stacking: C:F.307 ADP.4: 18 residues within 4Å: Chain D: D.15, G.17, S.18, V.20, K.22, Q.142, D.159, 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 D Hydrogen bonds: D:D.15, D:S.18, D:V.20, D:Q.142, D:D.162, D:D.162, D:D.162, D:K.218, D:E.219, D:G.303 Salt bridges: D:K.22, D:K.22 pi-Stacking: D:F.307 ADP.5: 17 residues within 4Å: Chain E: D.15, G.17, S.18, V.20, K.22, Q.142, D.159, G.161, D.162, K.218, E.219, G.302, G.303, S.304, L.306, F.307, L.337 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:S.18, E:V.20, E:Q.142, E:D.162, E:K.218, E:E.219, E:G.303 Salt bridges: E:K.22, E:K.22 pi-Stacking: E:F.307 ADP.6: 18 residues within 4Å: Chain F: D.15, G.17, S.18, V.20, K.22, Q.142, D.159, G.161, D.162, K.215, K.218, E.219, G.302, G.303, S.304, L.306, F.307, L.337 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:S.18, F:V.20, F:Q.142, F:Q.142, F:Q.142, F:D.162, F:D.162, F:D.162, F:K.218, F:E.219, F:G.303, F:L.337 Salt bridges: F:K.22, F:K.22 pi-Stacking: F:F.307 ADP.7: 18 residues within 4Å: Chain G: D.15, G.17, S.18, V.20, K.22, Q.142, D.159, G.161, D.162, K.215, K.218, E.219, G.302, G.303, S.304, L.306, F.307, L.337 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:D.15, G:S.18, G:Q.142, G:Q.142, G:D.162, G:K.215, G:K.218, G:E.219, G:G.303 Salt bridges: G:K.22, G:K.22 pi-Stacking: G:F.307 ADP.9: 16 residues within 4Å: Chain I: D.15, G.17, V.20, K.22, Q.142, D.159, G.161, D.162, K.215, K.218, E.219, G.302, G.303, S.304, L.306, L.337 9 PLIP interactions: 9 interactions with chain I Hydrogen bonds: I:Q.142, I:Q.142, I:D.162, I:D.162, I:K.218, I:G.303, I:L.337 Salt bridges: I:K.22, I:K.22 ADP.10: 17 residues within 4Å: Chain J: G.21, E.22, A.23, F.24, K.26, G.142, Y.143, H.172, E.208, K.211, V.212, G.308, T.309, M.311, N.351 Chain R: R.255, Q.262 12 PLIP interactions: 2 interactions with chain R, 10 interactions with chain J Hydrogen bonds: R:R.255, R:Q.262, J:E.22, J:A.23, J:Y.143, J:E.208, J:E.208, J:K.211, J:G.308, J:N.351 Salt bridges: J:K.26, J:K.26

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

ATP.8: 20 residues within 4Å: Chain H: D.11, G.13, S.14, G.15, M.16, K.18, Q.137, D.154, G.156, D.157, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336, V.339 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:G.15, H:M.16, H:Q.137, H:Q.137, H:D.154, H:D.157, H:D.157, H:K.213, H:G.302, H:M.305, H:K.336, H:K.336 Salt bridges: H:K.18, H:K.18, H:K.18, H:K.336

3 x ZN: ZINC ION(Non-covalent)

ZN.11: 4 residues within 4Å: Chain R: C.30, C.33, R.37, C.287 2 PLIP interactions: 2 interactions with chain R Metal complexes: R:C.33, R:C.287 ZN.12: 4 residues within 4Å: Chain R: C.51, C.54, C.70, C.73 2 PLIP interactions: 2 interactions with chain R Metal complexes: R:C.51, R:C.70 ZN.13: 4 residues within 4Å: Chain R: C.76, C.79, C.111, C.114 2 PLIP interactions: 2 interactions with chain R Metal complexes: R:C.76, R:C.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lau, C.K. et al., Cryo-EM reveals the complex architecture of dynactin's shoulder region and pointed end. Embo J. (2021)

Release Date

2020-07-29

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: MNTU
Dynactin subunit 3: OV
Dynactin 6: P
Dynactin subunit 5: Q
Dynactin subunit 4: R
Dynactin subunit 1: SW

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

T
m

U
n

O
O

V
o

P
U

Q
V

R
Y

S
Z

W
z

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 6

Dynactin subunit 5

Dynactin subunit 4

Dynactin subunit 1

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