SMTL ID : 7z8i.1

The barbed end complex of dynactin bound to BICDR1 and the cytoplasmic dynein tails (A2, B1, B2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-1-2-3-2-2-mer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: 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 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.18, A:G.19, A:V.20, A:V.20, A:D.162, A:D.162, A:K.218, A:E.219, A:E.219, A:G.303, A:L.306 Salt bridges: A:K.22, A:K.22 pi-Stacking: A:F.307 ADP.3: 17 residues within 4Å: Chain B: 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 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.18, B:G.19, B:D.162, B:D.162, B:D.162, B:K.218, B:E.219, B:E.219, B:G.303 Salt bridges: B:K.22, B:K.22 pi-Stacking: B:F.307 ADP.5: 17 residues within 4Å: Chain C: 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 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.18, C:G.19, C:V.20, 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.7: 17 residues within 4Å: Chain D: 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 Ligands: MG.8 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:S.18, D:G.19, D:V.20, D:D.162, D:D.162, D:K.218, D:E.219, D:G.303, D:L.337 Salt bridges: D:K.22, D:K.22 pi-Stacking: D:F.307 ADP.9: 17 residues within 4Å: Chain E: 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 Ligands: MG.10 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:S.18, E:G.19, E:V.20, E:D.162, E:D.162, 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.11: 17 residues within 4Å: Chain F: 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 Ligands: MG.12 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:S.18, F:G.19, F:V.20, F:V.20, F:D.162, F:D.162, F:K.215, F:K.215, F:K.218, F:E.219, F:G.303, F:L.306 Salt bridges: F:K.22, F:K.22 pi-Stacking: F:F.307

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 2 residues within 4Å: Chain A: Q.142 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain B: D.15, Q.142, T.340 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: D.15, Q.142 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain D: D.159 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain E: Q.142, D.159 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Ligands: ADP.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaaban, S. et al., Structure of dynein-dynactin on microtubules shows tandem adaptor binding. Nature (2022)

Release Date

2022-08-17

Peptides

ARP1 actin related protein 1 homolog A: ABCDEF
Capping protein (Actin filament) muscle Z-line, alpha 1: G
F-actin capping protein beta subunit: H
BICD family-like cargo adapter 1: IQ
Cytoplasmic dynein 1 heavy chain 1: JMN
Cytoplasmic dynein 1 intermediate chain 2: KO
Cytoplasmic dynein 1 light intermediate chain 2: LP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
K

H
L

I
X

Q
x

J
f

M
m

N
n

K
h

O
o

L
j

P
r

ARP1 actin related protein 1 homolog A

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

F-actin capping protein beta subunit

BICD family-like cargo adapter 1

Cytoplasmic dynein 1 heavy chain 1

Cytoplasmic dynein 1 intermediate chain 2

Cytoplasmic dynein 1 light intermediate chain 2

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