SMTL ID : 8ixe.1

GMPCPP-Alpha1C/Beta2A-microtubule decorated with kinesin seam region

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

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

GTP.1: 20 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, E.77, D.104, A.105, A.106, N.107, G.149, G.150, T.151, G.152, I.177, T.185, N.212, Y.230, N.234 Chain B: N.247, K.252 20 PLIP interactions: 17 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.11, A:E.77, A:D.104, A:A.105, A:A.106, A:N.107, A:G.150, A:T.151, A:T.151, 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: G.10, Q.11, A.12, Q.15, E.77, D.104, A.105, A.106, N.107, G.149, G.150, T.151, I.177, T.185, N.212, Y.230, N.234 Chain E: N.247, K.252 21 PLIP interactions: 18 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:Q.11, D:E.77, D:E.77, D:D.104, D:A.105, D:A.106, D:N.107, D:N.107, D:G.150, D:T.151, D:T.151, 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: 20 residues within 4Å: Chain G: G.10, Q.11, A.12, Q.15, E.77, D.104, A.105, A.106, N.107, G.149, G.150, T.151, I.177, T.185, N.212, Y.230, N.234 Chain H: L.246, N.247, K.252 22 PLIP interactions: 19 interactions with chain G, 3 interactions with chain H Hydrogen bonds: G:Q.11, G:E.77, G:E.77, G:D.104, G:A.105, G:A.106, G:N.107, G:N.107, G:G.150, G:T.151, G:T.151, G:T.185, G:N.212, G:N.212, G:N.234, G:N.234 pi-Stacking: G:Y.230, G:Y.230 pi-Cation interactions: G:Y.230 Salt bridges: H:K.252, H:K.252, H:K.252 GTP.10: 19 residues within 4Å: Chain J: G.10, Q.11, A.12, Q.15, E.77, D.104, A.105, A.106, N.107, G.149, G.150, T.151, I.177, T.185, N.212, Y.230, N.234 Chain K: N.247, K.252 20 PLIP interactions: 17 interactions with chain J, 3 interactions with chain K Hydrogen bonds: J:Q.11, J:E.77, J:D.104, J:A.105, J:A.106, J:N.107, J:G.150, J:T.151, J:T.151, 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

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

G2P.2: 15 residues within 4Å: Chain B: G.10, Q.11, C.12, N.99, S.138, G.140, T.143, G.144, D.177, E.181, N.204, Y.222, L.225, N.226 Chain D: E.260 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Q.11, B:C.12, B:A.97, B:N.99, B:S.138, B:G.142, B:T.143, B:T.143, B:G.144, B:D.177, B:D.177, B:T.178, B:T.178, B:N.204, B:N.226, D:E.260 pi-Stacking: B:Y.222, B:Y.222 G2P.5: 14 residues within 4Å: Chain E: G.10, Q.11, C.12, N.99, S.138, G.140, T.143, G.144, D.177, E.181, N.204, Y.222, L.225, N.226 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:Q.11, E:C.12, E:A.97, E:N.99, E:S.138, E:G.142, E:T.143, E:T.143, E:G.144, E:D.177, E:D.177, E:N.204, E:N.226 pi-Stacking: E:Y.222, E:Y.222 G2P.8: 14 residues within 4Å: Chain H: G.10, Q.11, C.12, N.99, S.138, G.140, T.143, G.144, D.177, E.181, N.204, Y.222, L.225, N.226 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:Q.11, H:C.12, H:N.99, H:S.138, H:G.142, H:T.143, H:T.143, H:G.144, H:D.177, H:N.204, H:N.226 pi-Stacking: H:Y.222, H:Y.222 G2P.11: 16 residues within 4Å: Chain G: E.260 Chain K: G.10, Q.11, C.12, N.99, S.138, G.140, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, L.225, N.226 19 PLIP interactions: 1 interactions with chain G, 18 interactions with chain K Hydrogen bonds: G:E.260, K:Q.11, K:C.12, K:A.97, K:N.99, K:N.99, K:S.138, K:G.142, K:T.143, K:T.143, K:G.144, K:D.177, K:D.177, K:T.178, K:T.178, K:N.204, K:N.226 pi-Stacking: K:Y.222, K:Y.222

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

ATP.3: 19 residues within 4Å: Chain C: R.37, R.39, P.40, N.42, Q.109, T.110, S.111, S.112, G.113, K.114, T.115, H.116, K.121, N.221, H.223, S.224, S.225, R.226, G.257 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:R.37, C:R.37, C:N.42, C:S.111, C:S.112, C:G.113, C:K.114, C:T.115, C:T.115, C:H.116, C:K.121, C:N.221, C:S.225, C:S.225, C:S.225, C:G.257 Salt bridges: C:K.114, C:K.114, C:R.226 pi-Stacking: C:H.116, C:H.116 ATP.6: 19 residues within 4Å: Chain F: R.37, R.39, P.40, N.42, Q.109, T.110, S.111, S.112, G.113, K.114, T.115, H.116, K.121, N.221, H.223, S.224, S.225, R.226, G.257 20 PLIP interactions: 20 interactions with chain F Hydrogen bonds: F:R.37, F:R.37, F:N.42, F:S.111, F:S.112, F:G.113, F:K.114, F:T.115, F:T.115, F:H.116, F:K.121, F:N.221, F:S.225, F:S.225, F:S.225, F:G.257 Salt bridges: F:K.114, F:K.114, F:R.226 pi-Stacking: F:H.116 ATP.9: 19 residues within 4Å: Chain I: R.37, R.39, P.40, N.42, Q.109, T.110, S.111, S.112, G.113, K.114, T.115, H.116, K.121, N.221, H.223, S.224, S.225, R.226, G.257 21 PLIP interactions: 21 interactions with chain I Hydrogen bonds: I:R.37, I:R.37, I:N.42, I:S.111, I:S.112, I:G.113, I:K.114, I:T.115, I:T.115, I:T.115, I:H.116, I:K.121, I:N.221, I:S.225, I:S.225, I:S.225, I:G.257 Salt bridges: I:K.114, I:K.114, I:R.226 pi-Stacking: I:H.116 ATP.12: 19 residues within 4Å: Chain L: R.37, R.39, P.40, N.42, Q.109, T.110, S.111, S.112, G.113, K.114, T.115, H.116, K.121, N.221, H.223, S.224, S.225, R.226, G.257 20 PLIP interactions: 20 interactions with chain L Hydrogen bonds: L:R.37, L:R.37, L:N.42, L:S.111, L:S.112, L:G.113, L:K.114, L:T.115, L:T.115, L:H.116, L:K.121, L:N.221, L:S.225, L:S.225, L:S.225, L:G.257 Salt bridges: L:K.114, L:K.114, L:R.226 pi-Stacking: L: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-1C chain: ADGJ
Tubulin beta-2A chain: BEHK
Kinesin-1 heavy chain: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

D
B

G
J

J
K

B
W

E
R

H
Z

K
a

C
l

F
h

I
p

L
q

Tubulin alpha-1C chain

Tubulin beta-2A chain

Kinesin-1 heavy chain

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