SMTL ID : 8ixf.1

GMPCPP-Alpha4A/Beta2A-microtubule decorated with kinesin non-seam region

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-9-9-9-mer

Ligands

9 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Covalent)

GTP.1: 19 residues within 4Å: Chain A: Q.11, A.12, Q.15, D.104, A.105, A.106, N.107, S.146, G.148, G.149, G.150, I.177, T.185, N.212, Y.230, N.234 Chain B: L.246, N.247, K.252 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.11, A:A.12, A:A.106, A:N.107, A:S.146, A:G.150, A:G.152, A:T.185, A:N.212, A:N.212, A:N.234, A:N.234 pi-Stacking: A:Y.230, A:Y.230 Salt bridges: B:K.252, B:K.252, B:K.252 GTP.4: 19 residues within 4Å: Chain D: Q.11, A.12, Q.15, D.104, A.105, A.106, N.107, S.146, G.148, G.149, G.150, I.177, T.185, N.212, Y.230, N.234 Chain E: L.246, N.247, K.252 17 PLIP interactions: 14 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:Q.11, D:A.12, D:A.106, D:N.107, D:S.146, D:G.150, D:G.152, D:T.185, D:N.212, D:N.212, D:N.234, D:N.234 pi-Stacking: D:Y.230, D:Y.230 Salt bridges: E:K.252, E:K.252, E:K.252 GTP.7: 19 residues within 4Å: Chain G: Q.11, A.12, Q.15, D.104, A.105, A.106, N.107, S.146, G.148, G.149, G.150, I.177, T.185, N.212, Y.230, N.234 Chain H: L.246, N.247, K.252 17 PLIP interactions: 14 interactions with chain G, 3 interactions with chain H Hydrogen bonds: G:Q.11, G:A.12, G:A.106, G:N.107, G:S.146, G:G.150, G:G.152, G:T.185, G:N.212, G:N.212, G:N.234, G:N.234 pi-Stacking: G:Y.230, G:Y.230 Salt bridges: H:K.252, H:K.252, H:K.252 GTP.10: 19 residues within 4Å: Chain J: Q.11, A.12, Q.15, D.104, A.105, A.106, N.107, S.146, G.148, G.149, G.150, I.177, T.185, N.212, Y.230, N.234 Chain K: L.246, N.247, K.252 17 PLIP interactions: 14 interactions with chain J, 3 interactions with chain K Hydrogen bonds: J:Q.11, J:A.12, J:A.106, J:N.107, J:S.146, J:G.150, J:G.152, J:T.185, J:N.212, J:N.212, J:N.234, J:N.234 pi-Stacking: J:Y.230, J:Y.230 Salt bridges: K:K.252, K:K.252, K:K.252 GTP.13: 19 residues within 4Å: Chain M: Q.11, A.12, Q.15, D.104, A.105, A.106, N.107, S.146, G.148, G.149, G.150, I.177, T.185, N.212, Y.230, N.234 Chain N: L.246, N.247, K.252 17 PLIP interactions: 14 interactions with chain M, 3 interactions with chain N Hydrogen bonds: M:Q.11, M:A.12, M:A.106, M:N.107, M:S.146, M:G.150, M:G.152, M:T.185, M:N.212, M:N.212, M:N.234, M:N.234 pi-Stacking: M:Y.230, M:Y.230 Salt bridges: N:K.252, N:K.252, N:K.252 GTP.16: 19 residues within 4Å: Chain P: Q.11, A.12, Q.15, D.104, A.105, A.106, N.107, S.146, G.148, G.149, G.150, I.177, T.185, N.212, Y.230, N.234 Chain Q: L.246, N.247, K.252 17 PLIP interactions: 14 interactions with chain P, 3 interactions with chain Q Hydrogen bonds: P:Q.11, P:A.12, P:A.106, P:N.107, P:S.146, P:G.150, P:G.152, P:T.185, P:N.212, P:N.212, P:N.234, P:N.234 pi-Stacking: P:Y.230, P:Y.230 Salt bridges: Q:K.252, Q:K.252, Q:K.252 GTP.19: 19 residues within 4Å: Chain S: Q.11, A.12, Q.15, D.104, A.105, A.106, N.107, S.146, G.148, G.149, G.150, I.177, T.185, N.212, Y.230, N.234 Chain T: L.246, N.247, K.252 17 PLIP interactions: 14 interactions with chain S, 3 interactions with chain T Hydrogen bonds: S:Q.11, S:A.12, S:A.106, S:N.107, S:S.146, S:G.150, S:G.152, S:T.185, S:N.212, S:N.212, S:N.234, S:N.234 pi-Stacking: S:Y.230, S:Y.230 Salt bridges: T:K.252, T:K.252, T:K.252 GTP.22: 19 residues within 4Å: Chain V: Q.11, A.12, Q.15, D.104, A.105, A.106, N.107, S.146, G.148, G.149, G.150, I.177, T.185, N.212, Y.230, N.234 Chain W: L.246, N.247, K.252 17 PLIP interactions: 14 interactions with chain V, 3 interactions with chain W Hydrogen bonds: V:Q.11, V:A.12, V:A.106, V:N.107, V:S.146, V:G.150, V:G.152, V:T.185, V:N.212, V:N.212, V:N.234, V:N.234 pi-Stacking: V:Y.230, V:Y.230 Salt bridges: W:K.252, W:K.252, W:K.252 GTP.25: 19 residues within 4Å: Chain Y: Q.11, A.12, Q.15, D.104, A.105, A.106, N.107, S.146, G.148, G.149, G.150, I.177, T.185, N.212, Y.230, N.234 Chain Z: L.246, N.247, K.252 17 PLIP interactions: 14 interactions with chain Y, 3 interactions with chain Z Hydrogen bonds: Y:Q.11, Y:A.12, Y:A.106, Y:N.107, Y:S.146, Y:G.150, Y:G.152, Y:T.185, Y:N.212, Y:N.212, Y:N.234, Y:N.234 pi-Stacking: Y:Y.230, Y:Y.230 Salt bridges: Z:K.252, Z:K.252, Z:K.252

9 x G2P: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

G2P.2: 16 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, N.99, S.138, T.143, G.144, D.177, N.204, L.207, Y.222, L.225, N.226 Chain G: L.254, E.260 13 PLIP interactions: 1 interactions with chain G, 12 interactions with chain B Hydrogen bonds: G:E.260, B:Q.11, B:Q.11, B:C.12, B:Q.15, B:G.98, B:N.99, B:S.138, B:G.144, B:D.177, B:Y.222, B:N.226, B:N.226 G2P.5: 17 residues within 4Å: Chain A: L.254, N.255, E.260 Chain E: G.10, Q.11, C.12, Q.15, N.99, S.138, T.143, G.144, D.177, N.204, L.207, Y.222, L.225, N.226 13 PLIP interactions: 12 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:Q.11, E:Q.11, E:C.12, E:Q.15, E:G.98, E:N.99, E:S.138, E:G.144, E:D.177, E:Y.222, E:N.226, E:N.226, A:E.260 G2P.8: 14 residues within 4Å: Chain H: G.10, Q.11, C.12, Q.15, N.99, S.138, T.143, G.144, D.177, N.204, L.207, Y.222, L.225, N.226 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:Q.11, H:Q.11, H:C.12, H:Q.15, H:G.98, H:N.99, H:S.138, H:G.144, H:D.177, H:Y.222, H:N.226, H:N.226 G2P.11: 14 residues within 4Å: Chain K: G.10, Q.11, C.12, Q.15, N.99, S.138, T.143, G.144, D.177, N.204, L.207, Y.222, L.225, N.226 12 PLIP interactions: 12 interactions with chain K Hydrogen bonds: K:Q.11, K:Q.11, K:C.12, K:Q.15, K:G.98, K:N.99, K:S.138, K:G.144, K:D.177, K:Y.222, K:N.226, K:N.226 G2P.14: 15 residues within 4Å: Chain J: L.254, E.260 Chain N: Q.11, C.12, Q.15, N.99, S.138, T.143, G.144, D.177, N.204, L.207, Y.222, L.225, N.226 13 PLIP interactions: 12 interactions with chain N, 1 interactions with chain J Hydrogen bonds: N:Q.11, N:Q.11, N:C.12, N:Q.15, N:G.98, N:N.99, N:S.138, N:G.144, N:D.177, N:Y.222, N:N.226, N:N.226, J:E.260 G2P.17: 16 residues within 4Å: Chain M: L.254, N.255, E.260 Chain Q: Q.11, C.12, Q.15, N.99, S.138, T.143, G.144, D.177, N.204, L.207, Y.222, L.225, N.226 13 PLIP interactions: 12 interactions with chain Q, 1 interactions with chain M Hydrogen bonds: Q:Q.11, Q:Q.11, Q:C.12, Q:Q.15, Q:G.98, Q:N.99, Q:S.138, Q:G.144, Q:D.177, Q:Y.222, Q:N.226, Q:N.226, M:E.260 G2P.20: 14 residues within 4Å: Chain T: G.10, Q.11, C.12, Q.15, N.99, S.138, T.143, G.144, D.177, N.204, L.207, Y.222, L.225, N.226 12 PLIP interactions: 12 interactions with chain T Hydrogen bonds: T:Q.11, T:Q.11, T:C.12, T:Q.15, T:G.98, T:N.99, T:S.138, T:G.144, T:D.177, T:Y.222, T:N.226, T:N.226 G2P.23: 16 residues within 4Å: Chain S: L.254, E.260 Chain W: G.10, Q.11, C.12, Q.15, N.99, S.138, T.143, G.144, D.177, N.204, L.207, Y.222, L.225, N.226 13 PLIP interactions: 12 interactions with chain W, 1 interactions with chain S Hydrogen bonds: W:Q.11, W:Q.11, W:C.12, W:Q.15, W:G.98, W:N.99, W:S.138, W:G.144, W:D.177, W:Y.222, W:N.226, W:N.226, S:E.260 G2P.26: 16 residues within 4Å: Chain V: L.254, N.255, E.260 Chain Z: Q.11, C.12, Q.15, N.99, S.138, T.143, G.144, D.177, N.204, L.207, Y.222, L.225, N.226 13 PLIP interactions: 12 interactions with chain Z, 1 interactions with chain V Hydrogen bonds: Z:Q.11, Z:Q.11, Z:C.12, Z:Q.15, Z:G.98, Z:N.99, Z:S.138, Z:G.144, Z:D.177, Z:Y.222, Z:N.226, Z:N.226, V:E.260

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

ATP.3: 17 residues within 4Å: Chain C: R.37, R.39, P.40, Q.109, T.110, S.111, S.112, G.113, K.114, T.115, H.116, N.221, H.223, S.224, S.225, L.255, G.257 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:R.37, C:R.37, C:S.111, C:S.112, C:G.113, C:K.114, C:T.115, C:T.115, C:H.116, C:H.116, C:N.221, C:S.225, C:S.225, C:L.255, C:G.257 Salt bridges: C:K.114, C:K.114 pi-Cation interactions: C:H.116, C:H.116 ATP.6: 17 residues within 4Å: Chain F: R.37, R.39, P.40, Q.109, T.110, S.111, S.112, G.113, K.114, T.115, H.116, N.221, H.223, S.224, S.225, L.255, G.257 19 PLIP interactions: 19 interactions with chain F Hydrogen bonds: F:R.37, F:R.37, F:S.111, F:S.112, F:G.113, F:K.114, F:T.115, F:T.115, F:H.116, F:H.116, F:N.221, F:S.225, F:S.225, F:L.255, F:G.257 Salt bridges: F:K.114, F:K.114 pi-Cation interactions: F:H.116, F:H.116 ATP.9: 17 residues within 4Å: Chain I: R.37, R.39, P.40, Q.109, T.110, S.111, S.112, G.113, K.114, T.115, H.116, N.221, H.223, S.224, S.225, L.255, G.257 19 PLIP interactions: 19 interactions with chain I Hydrogen bonds: I:R.37, I:R.37, I:S.111, I:S.112, I:G.113, I:K.114, I:T.115, I:T.115, I:H.116, I:H.116, I:N.221, I:S.225, I:S.225, I:L.255, I:G.257 Salt bridges: I:K.114, I:K.114 pi-Cation interactions: I:H.116, I:H.116 ATP.12: 17 residues within 4Å: Chain L: R.37, R.39, P.40, Q.109, T.110, S.111, S.112, G.113, K.114, T.115, H.116, N.221, H.223, S.224, S.225, L.255, G.257 19 PLIP interactions: 19 interactions with chain L Hydrogen bonds: L:R.37, L:R.37, L:S.111, L:S.112, L:G.113, L:K.114, L:T.115, L:T.115, L:H.116, L:H.116, L:N.221, L:S.225, L:S.225, L:L.255, L:G.257 Salt bridges: L:K.114, L:K.114 pi-Cation interactions: L:H.116, L:H.116 ATP.15: 17 residues within 4Å: Chain O: R.37, R.39, P.40, Q.109, T.110, S.111, S.112, G.113, K.114, T.115, H.116, N.221, H.223, S.224, S.225, L.255, G.257 19 PLIP interactions: 19 interactions with chain O Hydrogen bonds: O:R.37, O:R.37, O:S.111, O:S.112, O:G.113, O:K.114, O:T.115, O:T.115, O:H.116, O:H.116, O:N.221, O:S.225, O:S.225, O:L.255, O:G.257 Salt bridges: O:K.114, O:K.114 pi-Cation interactions: O:H.116, O:H.116 ATP.18: 17 residues within 4Å: Chain R: R.37, R.39, P.40, Q.109, T.110, S.111, S.112, G.113, K.114, T.115, H.116, N.221, H.223, S.224, S.225, L.255, G.257 19 PLIP interactions: 19 interactions with chain R Hydrogen bonds: R:R.37, R:R.37, R:S.111, R:S.112, R:G.113, R:K.114, R:T.115, R:T.115, R:H.116, R:H.116, R:N.221, R:S.225, R:S.225, R:L.255, R:G.257 Salt bridges: R:K.114, R:K.114 pi-Cation interactions: R:H.116, R:H.116 ATP.21: 17 residues within 4Å: Chain U: R.37, R.39, P.40, Q.109, T.110, S.111, S.112, G.113, K.114, T.115, H.116, N.221, H.223, S.224, S.225, L.255, G.257 19 PLIP interactions: 19 interactions with chain U Hydrogen bonds: U:R.37, U:R.37, U:S.111, U:S.112, U:G.113, U:K.114, U:T.115, U:T.115, U:H.116, U:H.116, U:N.221, U:S.225, U:S.225, U:L.255, U:G.257 Salt bridges: U:K.114, U:K.114 pi-Cation interactions: U:H.116, U:H.116 ATP.24: 17 residues within 4Å: Chain X: R.37, R.39, P.40, Q.109, T.110, S.111, S.112, G.113, K.114, T.115, H.116, N.221, H.223, S.224, S.225, L.255, G.257 19 PLIP interactions: 19 interactions with chain X Hydrogen bonds: X:R.37, X:R.37, X:S.111, X:S.112, X:G.113, X:K.114, X:T.115, X:T.115, X:H.116, X:H.116, X:N.221, X:S.225, X:S.225, X:L.255, X:G.257 Salt bridges: X:K.114, X:K.114 pi-Cation interactions: X:H.116, X:H.116 ATP.27: 17 residues within 4Å: Chain 0: R.37, R.39, P.40, Q.109, T.110, S.111, S.112, G.113, K.114, T.115, H.116, N.221, H.223, S.224, S.225, L.255, G.257 19 PLIP interactions: 19 interactions with chain 0 Hydrogen bonds: 0:R.37, 0:R.37, 0:S.111, 0:S.112, 0:G.113, 0:K.114, 0:T.115, 0:T.115, 0:H.116, 0:H.116, 0:N.221, 0:S.225, 0:S.225, 0:L.255, 0:G.257 Salt bridges: 0:K.114, 0:K.114 pi-Cation interactions: 0:H.116, 0:H.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diao, L. et al., Cryo-EM of alpha-tubulin isotype-containing microtubules revealed a contracted structure of alpha 4A/ beta 2A microtubules. Acta Biochim.Biophys.Sin. (2023)

Release Date

2023-08-16

Peptides

Tubulin alpha-4A chain: ADGJMPSVY
Tubulin beta-2A chain: BEHKNQTWZ
Kinesin-1 heavy chain: CFILORUX0

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

D
A

G
B

J
C

M
D

P
E

S
F

V
G

Y
H

B
Q

E
J

H
K

K
L

N
M

Q
N

T
O

W
P

Z
R

C
Y

F
S

I
T

L
U

O
V

R
W

U
X

X
Z

0
a

Tubulin alpha-4A chain

Tubulin beta-2A chain

Kinesin-1 heavy chain

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