SMTL ID : 9i8g.1

Inwards conformation' of the human gamma-TuRC from purified centrosomes obtained by rigid body docking

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-6-2-1-2-1-2-14-mer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.1: 13 residues within 4Å: Chain O: G.14, S.15, G.16, M.17, G.157, D.158, G.183, R.184, E.215, G.302, G.303, T.304, M.306 6 PLIP interactions: 6 interactions with chain O Hydrogen bonds: O:S.15, O:G.16, O:M.17, O:M.17, O:D.158, O:G.303

14 x GDP: GUANOSINE-5'-DIPHOSPHATE

GDP.2: 14 residues within 4Å: Chain T: G.11, Q.12, C.13, Q.16, G.101, S.140, A.142, G.144, T.145, G.146, V.171, N.207, F.225, N.229 11 PLIP interactions: 11 interactions with chain T Hydrogen bonds: T:Q.12, T:G.101, T:S.140, T:G.144, T:T.145, T:G.146, T:N.207, T:N.207, T:N.229, T:N.229 pi-Stacking: T:F.225 GDP.3: 12 residues within 4Å: Chain U: Q.12, C.13, Q.16, S.140, A.142, G.144, T.145, G.146, V.171, N.207, F.225, N.229 11 PLIP interactions: 11 interactions with chain U Hydrogen bonds: U:Q.12, U:S.140, U:T.145, U:T.145, U:G.146, U:N.207, U:N.207, U:N.229, U:N.229 pi-Stacking: U:F.225, U:F.225 GDP.4: 13 residues within 4Å: Chain V: G.11, Q.12, C.13, Q.16, G.101, S.140, A.142, G.144, T.145, G.146, N.207, F.225, N.229 12 PLIP interactions: 12 interactions with chain V Hydrogen bonds: V:G.101, V:S.140, V:G.144, V:T.145, V:G.146, V:N.207, V:N.207, V:N.229, V:N.229 pi-Stacking: V:F.225, V:F.225 pi-Cation interactions: V:F.225 GDP.5: 14 residues within 4Å: Chain W: G.11, Q.12, C.13, Q.16, G.101, S.140, A.142, G.144, T.145, G.146, V.171, N.207, F.225, N.229 11 PLIP interactions: 11 interactions with chain W Hydrogen bonds: W:Q.12, W:S.140, W:T.145, W:T.145, W:G.146, W:N.207, W:N.207, W:N.229, W:N.229 pi-Stacking: W:F.225, W:F.225 GDP.6: 14 residues within 4Å: Chain X: G.11, Q.12, C.13, Q.16, G.101, S.140, A.142, G.144, T.145, G.146, V.171, N.207, F.225, N.229 11 PLIP interactions: 11 interactions with chain X Hydrogen bonds: X:Q.12, X:G.101, X:S.140, X:G.144, X:T.145, X:G.146, X:N.207, X:N.207, X:N.229, X:N.229 pi-Stacking: X:F.225 GDP.7: 13 residues within 4Å: Chain Y: G.11, Q.12, C.13, Q.16, S.140, A.142, G.144, T.145, G.146, V.171, N.207, F.225, N.229 11 PLIP interactions: 11 interactions with chain Y Hydrogen bonds: Y:Q.12, Y:S.140, Y:T.145, Y:T.145, Y:G.146, Y:N.207, Y:N.207, Y:N.229, Y:N.229 pi-Stacking: Y:F.225, Y:F.225 GDP.8: 13 residues within 4Å: Chain Z: G.11, Q.12, C.13, Q.16, G.101, S.140, A.142, G.144, T.145, G.146, N.207, F.225, N.229 12 PLIP interactions: 12 interactions with chain Z Hydrogen bonds: Z:G.101, Z:S.140, Z:G.144, Z:T.145, Z:G.146, Z:N.207, Z:N.207, Z:N.229, Z:N.229 pi-Stacking: Z:F.225, Z:F.225 pi-Cation interactions: Z:F.225 GDP.9: 12 residues within 4Å: Chain 0: Q.12, C.13, Q.16, S.140, A.142, G.144, T.145, G.146, V.171, N.207, F.225, N.229 11 PLIP interactions: 11 interactions with chain 0 Hydrogen bonds: 0:Q.12, 0:S.140, 0:T.145, 0:T.145, 0:G.146, 0:N.207, 0:N.207, 0:N.229, 0:N.229 pi-Stacking: 0:F.225, 0:F.225 GDP.10: 14 residues within 4Å: Chain 1: G.11, Q.12, C.13, Q.16, G.101, N.102, S.140, A.142, G.144, T.145, N.207, F.225, I.228, N.229 11 PLIP interactions: 11 interactions with chain 1 Hydrogen bonds: 1:Q.12, 1:G.101, 1:S.140, 1:G.144, 1:T.145, 1:N.207, 1:N.229, 1:N.229 pi-Stacking: 1:F.225, 1:F.225 pi-Cation interactions: 1:F.225 GDP.11: 14 residues within 4Å: Chain 2: G.11, Q.12, C.13, Q.16, N.102, S.140, A.142, G.144, T.145, G.146, N.207, F.225, I.228, N.229 13 PLIP interactions: 13 interactions with chain 2 Hydrogen bonds: 2:Q.12, 2:S.140, 2:G.144, 2:T.145, 2:T.145, 2:T.145, 2:G.146, 2:N.207, 2:N.207, 2:N.229, 2:N.229 pi-Stacking: 2:F.225, 2:F.225 GDP.12: 10 residues within 4Å: Chain 3: Q.12, C.13, Q.16, A.142, G.143, G.144, T.145, N.207, F.225, N.229 9 PLIP interactions: 9 interactions with chain 3 Hydrogen bonds: 3:Q.12, 3:G.144, 3:T.145, 3:N.207, 3:N.207, 3:N.229, 3:N.229 pi-Stacking: 3:F.225, 3:F.225 GDP.13: 12 residues within 4Å: Chain 4: G.11, Q.12, C.13, Q.16, S.140, A.142, G.144, T.145, G.146, N.207, F.225, N.229 10 PLIP interactions: 10 interactions with chain 4 Hydrogen bonds: 4:Q.12, 4:S.140, 4:A.142, 4:T.145, 4:T.145, 4:G.146, 4:N.207, 4:N.229, 4:N.229 pi-Stacking: 4:F.225 GDP.14: 13 residues within 4Å: Chain 5: G.11, Q.12, C.13, Q.16, G.101, S.140, A.142, G.144, T.145, G.146, N.207, F.225, N.229 12 PLIP interactions: 12 interactions with chain 5 Hydrogen bonds: 5:G.101, 5:S.140, 5:G.144, 5:T.145, 5:G.146, 5:N.207, 5:N.207, 5:N.229, 5:N.229 pi-Stacking: 5:F.225, 5:F.225 pi-Cation interactions: 5:F.225 GDP.15: 9 residues within 4Å: Chain 6: Q.12, C.13, G.101, A.142, G.143, G.144, T.145, G.146, F.225 3 PLIP interactions: 3 interactions with chain 6 Hydrogen bonds: 6:G.101, 6:T.145, 6:G.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, Q. et al., Structural mechanisms for centrosomal recruitment and organization of the microtubule nucleator gamma-TuRC. Nat Commun (2025)

Release Date

2025-03-19

Peptides

Gamma-tubulin complex component 2: ACEGM
Gamma-tubulin complex component 3: BDFHNR
Gamma-tubulin complex component 4: IK
Gamma-tubulin complex component 5: J
Gamma-tubulin complex component 6: LP
Actin, cytoplasmic 1: O
Mitotic-spindle organizing protein 1: QS
Tubulin gamma-1 chain: TUVWXYZ0123456

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

M
M

B
B

D
D

F
F

H
H

N
T

R
R

I
I

K
K

J
J

L
L

P
P

O
U

Q
Q

S
S

T
a

U
b

V
c

W
d

X
e

Y
f

Z
g

0
h

1
i

2
j

3
k

4
l

5
m

6
t

Gamma-tubulin complex component 2

Gamma-tubulin complex component 3

Gamma-tubulin complex component 4

Gamma-tubulin complex component 5

Gamma-tubulin complex component 6

Actin, cytoplasmic 1

Mitotic-spindle organizing protein 1

Tubulin gamma-1 chain

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