SMTL ID : 5afu.1

Cryo-EM structure of dynein tail-dynactin-BICD2N complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 8.20 Å

Oligo State

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

Ligands

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

ADP.1: 15 residues within 4Å: Chain G: G.11, S.12, G.13, V.14, K.16, G.155, D.156, K.209, K.212, E.213, G.296, G.297, S.298, L.300, F.301 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:S.12, G:G.13, G:D.156, G:K.212, G:E.213, G:G.297 Salt bridges: G:K.16, G:K.16 pi-Stacking: G:F.301 ADP.2: 16 residues within 4Å: Chain H: G.11, S.12, G.13, V.14, K.16, G.155, D.156, K.209, K.212, E.213, G.296, G.297, S.298, L.300, F.301, L.331 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:S.12, H:S.12, H:G.13, H:V.14, H:V.14, H:D.156, H:K.209, H:K.212, H:E.213, H:G.297 Salt bridges: H:K.16, H:K.16 pi-Stacking: H:F.301 ADP.3: 15 residues within 4Å: Chain I: G.11, S.12, G.13, V.14, K.16, G.155, D.156, K.209, K.212, E.213, G.296, G.297, L.300, F.301, L.331 14 PLIP interactions: 14 interactions with chain I Hydrogen bonds: I:G.11, I:S.12, I:S.12, I:G.13, I:V.14, I:V.14, I:D.156, I:K.209, I:K.212, I:E.213, I:G.297 Salt bridges: I:K.16, I:K.16 pi-Stacking: I:F.301 ADP.4: 14 residues within 4Å: Chain J: G.11, S.12, G.13, V.14, G.155, D.156, K.209, K.212, E.213, G.296, G.297, S.298, L.300, F.301 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:G.11, J:S.12, J:G.13, J:V.14, J:D.156, J:K.212, J:E.213, J:E.213, J:G.297 Salt bridges: J:K.16 pi-Stacking: J:F.301 ADP.5: 15 residues within 4Å: Chain K: G.11, S.12, G.13, V.14, K.16, G.155, D.156, K.209, K.212, E.213, G.296, G.297, L.300, F.301, L.331 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:S.12, K:G.13, K:V.14, K:V.14, K:D.156, K:K.212, K:G.297, K:L.300 Salt bridges: K:K.16, K:K.16 pi-Stacking: K:F.301 ADP.6: 15 residues within 4Å: Chain L: G.11, S.12, G.13, V.14, K.16, G.155, D.156, K.209, K.212, E.213, G.296, G.297, S.298, L.300, F.301 13 PLIP interactions: 13 interactions with chain L Hydrogen bonds: L:G.11, L:S.12, L:G.13, L:V.14, L:D.156, L:D.156, L:D.156, L:K.212, L:E.213, L:G.297 Salt bridges: L:K.16, L:K.16 pi-Stacking: L:F.301 ADP.7: 17 residues within 4Å: Chain M: G.11, S.12, G.13, V.14, K.16, G.155, D.156, G.157, K.209, K.212, E.213, G.296, G.297, S.298, L.300, F.301, L.331 12 PLIP interactions: 12 interactions with chain M Hydrogen bonds: M:G.11, M:S.12, M:G.13, M:V.14, M:D.156, M:G.157, M:K.212, M:E.213, M:G.297 Salt bridges: M:K.16, M:K.16 pi-Stacking: M:F.301 ADP.9: 16 residues within 4Å: Chain O: G.11, S.12, G.13, V.14, G.155, D.156, G.157, K.209, K.212, E.213, G.296, G.297, S.298, L.300, F.301, L.331 10 PLIP interactions: 10 interactions with chain O Hydrogen bonds: O:S.12, O:G.13, O:V.14, O:V.14, O:D.156, O:G.157, O:K.212, O:E.213, O:G.297 pi-Stacking: O:F.301 ADP.10: 16 residues within 4Å: Chain P: G.10, E.11, A.12, F.13, K.15, G.131, Y.132, H.161, E.197, K.200, V.201, G.296, G.297, T.298, M.300, N.340 11 PLIP interactions: 11 interactions with chain P Hydrogen bonds: P:E.11, P:A.12, P:F.13, P:F.13, P:Y.132, P:E.197, P:K.200, P:G.297, P:N.340 Salt bridges: P:K.15, P:K.15

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

ATP.8: 18 residues within 4Å: Chain N: D.6, G.8, S.9, G.10, M.11, K.13, Q.132, G.151, D.152, R.205, K.208, E.209, G.296, G.297, T.298, M.300, Y.301, K.331 15 PLIP interactions: 15 interactions with chain N Hydrogen bonds: N:S.9, N:G.10, N:M.11, N:Q.132, N:Q.132, N:D.152, N:D.152, N:D.152, N:K.208, N:G.297, N:M.300 Salt bridges: N:K.13, N:K.13, N:K.13 pi-Stacking: N:Y.301

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Urnavicius, L. et al., The Structure of the Dynactin Complex and its Interaction with Dynein. Science (2015)

Release Date

2015-03-11

Peptides

DYNEIN TAIL: A
DYNEIN TAIL: B
DYNEIN TAIL: CD
DYNEIN TAIL: EF
DYNACTIN: GHIJKLMO
ACTIN, CYTOPLASMIC 1: N
DYNACTIN: P
CAPPING PROTEIN (ACTIN FILAMENT) MUSCLE Z-LINE, ALPHA 1: Q
F-ACTIN CAPPING PROTEIN BETA SUBUNIT VARIANT II: R
DYNACTIN: S
DYNACTIN 6: T
DYNACTIN: UV
DYNACTIN: WX
DYNACTIN: Y
DYNACTIN: Z
F-ACTIN-CAPPING PROTEIN SUBUNIT BETA: 0
F-ACTIN-CAPPING PROTEIN SUBUNIT BETA: 1
DYNACTIN: 2
DYNACTIN: 3
DYNACTIN: 4
DYNACTIN: 5
F-ACTIN-CAPPING PROTEIN SUBUNIT BETA: 6

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
5

F
6

G
A

H
B

I
C

J
D

K
E

L
F

M
G

O
I

N
H

P
J

Q
K

R
L

S
M

T
N

U
O

V
P

W
Q

X
R

Y
U

Z
V

0
Y

1
Z

2
a

3
b

4
c

5
d

6
z

DYNEIN TAIL

DYNEIN TAIL

DYNEIN TAIL

DYNEIN TAIL

DYNACTIN

ACTIN, CYTOPLASMIC 1

DYNACTIN

CAPPING PROTEIN (ACTIN FILAMENT) MUSCLE Z-LINE, ALPHA 1

F-ACTIN CAPPING PROTEIN BETA SUBUNIT VARIANT II

DYNACTIN

DYNACTIN 6

DYNACTIN

DYNACTIN

DYNACTIN

DYNACTIN

F-ACTIN-CAPPING PROTEIN SUBUNIT BETA

F-ACTIN-CAPPING PROTEIN SUBUNIT BETA

DYNACTIN

DYNACTIN

DYNACTIN

DYNACTIN

F-ACTIN-CAPPING PROTEIN SUBUNIT BETA

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