SMTL ID : 9b7j.1

Cryo-EM structure of human dynactin complex bound to Chlamydia effector Dre1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

8 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, G.161, D.162, G.163, G.187, K.215, K.218, E.219, G.303, S.304, L.306, F.307, L.337 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.18, A:S.18, A:V.20, A:D.162, A:D.162, A:D.162, A:D.162, A:K.218, A:G.303 Salt bridges: A:K.22, A:K.22 ADP.2: 17 residues within 4Å: Chain B: G.17, S.18, G.19, V.20, K.22, G.161, D.162, G.163, G.187, K.218, E.219, G.303, S.304, L.306, F.307, L.337 Chain V: Y.81 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain V Hydrogen bonds: B:S.18, B:G.19, B:V.20, B:D.162, B:D.162, B:K.218, B:E.219, B:G.303, V:Y.81 Salt bridges: B:K.22, B:K.22 pi-Stacking: B:F.307 ADP.3: 19 residues within 4Å: Chain C: G.17, S.18, G.19, V.20, K.22, Q.142, G.161, D.162, G.163, G.187, K.215, K.218, E.219, G.303, S.304, L.306, F.307, L.337 Chain W: E.36 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain W Hydrogen bonds: C:S.18, C:S.18, C:G.19, C:D.162, C:D.162, C:D.162, C:D.162, C:K.218, C:G.303, W:E.36 Salt bridges: C:K.22, C:K.22 pi-Stacking: C:F.307 ADP.4: 17 residues within 4Å: Chain D: G.17, S.18, G.19, V.20, K.22, G.161, D.162, G.163, G.187, K.215, K.218, E.219, G.303, S.304, L.306, F.307, L.337 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:S.18, D:D.162, D:D.162, D:D.162, D:K.215, D:K.218, D:G.303 Salt bridges: D:K.22, D:K.22 pi-Stacking: D:F.307 ADP.5: 17 residues within 4Å: Chain E: G.17, S.18, G.19, V.20, K.22, G.161, D.162, G.163, G.187, K.215, K.218, E.219, G.303, S.304, L.306, F.307, L.337 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:S.18, E:D.162, E:D.162, E:D.162, E:D.162, E:K.218, E:G.303 Salt bridges: E:K.22, E:K.22 pi-Stacking: E:F.307 ADP.6: 17 residues within 4Å: Chain F: G.17, S.18, G.19, V.20, K.22, G.161, D.162, G.163, G.187, K.215, K.218, E.219, G.303, S.304, L.306, F.307, L.337 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:S.18, F:S.18, F:V.20, F:D.162, F:D.162, F:D.162, F:K.218, F:G.303 Salt bridges: F:K.22, F:K.22 pi-Stacking: F:F.307 ADP.7: 18 residues within 4Å: Chain G: G.17, S.18, G.19, K.22, Q.142, G.161, D.162, G.163, 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 G Hydrogen bonds: G:S.18, G:D.162, G:D.162, G:D.162, G:D.162, G:K.218, G:E.219, G:G.303 Salt bridges: G:K.22, G:K.22 pi-Stacking: G:F.307 ADP.9: 19 residues within 4Å: Chain I: G.17, S.18, G.19, V.20, K.22, G.161, D.162, G.187, S.191, K.215, K.218, E.219, C.222, G.302, G.303, S.304, L.306, F.307, L.337 11 PLIP interactions: 11 interactions with chain I Hydrogen bonds: I:D.15, I:S.18, I:D.162, I:D.162, I:D.162, I:K.218, I:E.219, I:G.303 Salt bridges: I:K.22, I:K.22 pi-Stacking: I:F.307

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.8: 18 residues within 4Å: Chain H: D.11, G.13, S.14, G.15, M.16, K.18, G.156, D.157, G.158, G.182, R.210, K.213, E.214, G.302, T.303, M.305, Y.306, K.336 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:S.14, H:G.15, H:M.16, H:M.16, H:K.18, H:D.157, H:D.157, H:D.157, H:D.157, H:K.213, H:G.302

3 x ZN: ZINC ION(Non-covalent)

ZN.10: 3 residues within 4Å: Chain K: Q.15, G.16, E.35 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:Q.15, K:E.35, K:E.35 ZN.11: 3 residues within 4Å: Chain K: C.54, E.56, N.72 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:E.56, K:E.56 ZN.12: 6 residues within 4Å: Chain K: C.76, C.79, H.81, C.111, C.114, W.116 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.76, K:C.79, K:C.111, K:C.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sherry, J. et al., The Chlamydia effector Dre1 binds dynactin to reposition host organelles during infection. Cell Rep (2025)

Release Date

2025-04-16

Peptides

Alpha-centractin: ABCDEFGI
Actin, cytoplasmic 1: H
Actin-related protein 10: J
Dynactin subunit 4: K
Dynactin subunit 5: L
Dynactin subunit 6: M
F-actin-capping protein subunit alpha-1: N
F-actin-capping protein subunit beta: O
Dynactin subunit 2: PQVW
Dynactin subunit 3: RX
Dynactin subunit 1: S
Dynactin subunit 1, p150-glued: T
Dynactin subunit 2, p50 dynamitin: U
Dynactin subunit 1: Y

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

V
p

W
q

R
R

X
r

S
S

T
T

U
U

Y
s

Alpha-centractin

Actin, cytoplasmic 1

Actin-related protein 10

Dynactin subunit 4

Dynactin subunit 5

Dynactin subunit 6

F-actin-capping protein subunit alpha-1

F-actin-capping protein subunit beta

Dynactin subunit 2

Dynactin subunit 3

Dynactin subunit 1

Dynactin subunit 1, p150-glued

Dynactin subunit 2, p50 dynamitin

Dynactin subunit 1

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