SMTL ID : 8ixb.1

GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin seam region

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

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

GTP.1: 19 residues within 4Å: Chain A: Q.11, A.12, Q.15, E.77, D.104, A.105, A.106, N.107, G.149, G.150, I.177, T.185, E.189, Y.230, L.233, 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:Q.11, A:E.77, A:A.105, A:A.106, A:N.107, A:N.107, A:S.146, A:G.150, A:E.189, A:N.234, A:N.234 pi-Stacking: A:Y.230 pi-Cation interactions: A:Y.230 Salt bridges: B:K.252, B:K.252, B:K.252 GTP.4: 20 residues within 4Å: Chain D: Q.11, A.12, Q.15, E.77, D.104, A.105, A.106, N.107, S.146, G.149, G.150, I.177, T.185, E.189, Y.230, L.233, N.234 Chain E: L.246, N.247, K.252 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:Q.11, D:A.12, D:E.77, D:A.105, D:A.106, D:N.107, D:N.107, D:S.146, D:G.150, D:E.189, D:N.234 pi-Stacking: D:Y.230 pi-Cation interactions: 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, E.77, D.104, A.105, A.106, N.107, G.149, G.150, I.177, T.185, E.189, Y.230, L.233, N.234 Chain H: L.246, N.247, K.252 15 PLIP interactions: 12 interactions with chain G, 3 interactions with chain H Hydrogen bonds: G:Q.11, G:E.77, G:A.105, G:A.106, G:N.107, G:N.107, G:S.146, G:G.150, G:E.189, G:N.234 pi-Stacking: G:Y.230 pi-Cation interactions: G:Y.230 Salt bridges: H:K.252, H:K.252, H:K.252 GTP.10: 20 residues within 4Å: Chain J: Q.11, A.12, Q.15, E.77, D.104, A.105, A.106, N.107, S.146, G.149, G.150, I.177, T.185, E.189, Y.230, L.233, N.234 Chain K: L.246, N.247, K.252 16 PLIP interactions: 13 interactions with chain J, 3 interactions with chain K Hydrogen bonds: J:Q.11, J:A.12, J:E.77, J:A.105, J:A.106, J:N.107, J:N.107, J:S.146, J:G.150, J:E.189, J:N.234 pi-Stacking: J:Y.230 pi-Cation interactions: 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: 14 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, S.138, G.140, T.143, G.144, D.177, N.204, L.207, Y.222, N.226 Chain D: E.260 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:N.99, B:S.138, B:T.143, B:T.143, B:G.144, B:D.177, B:D.177, B:N.204, B:N.204, B:N.226, B:N.226, D:N.255, D:E.260 G2P.5: 13 residues within 4Å: Chain E: G.10, Q.11, C.12, Q.15, S.138, G.140, T.143, G.144, D.177, N.204, L.207, Y.222, N.226 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:Q.11, E:Q.11, E:C.12, E:N.99, E:S.138, E:T.143, E:T.143, E:G.144, E:D.177, E:D.177, E:N.204, E:N.204, E:N.226, E:N.226 G2P.8: 14 residues within 4Å: Chain H: G.10, Q.11, C.12, Q.15, N.99, S.138, G.140, T.143, G.144, D.177, N.204, L.207, Y.222, N.226 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:Q.11, H:Q.11, H:C.12, H:N.99, H:S.138, H:T.143, H:G.144, H:D.177, H:D.177, H:N.204, H:N.204, H:N.226, H:N.226 G2P.11: 15 residues within 4Å: Chain G: E.260 Chain K: G.10, Q.11, C.12, Q.15, N.99, S.138, G.140, T.143, G.144, D.177, N.204, L.207, Y.222, N.226 16 PLIP interactions: 15 interactions with chain K, 1 interactions with chain G Hydrogen bonds: K:Q.11, K:Q.11, K:C.12, K:N.99, K:S.138, K:T.143, K:T.143, K:G.144, K:D.177, K:D.177, K:N.204, K:N.204, K:N.226, K:N.226, G:E.260 pi-Stacking: 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, N.221, H.223, S.225, R.226, L.255, A.256, G.257 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: 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:T.115, C:H.116, C:N.221, C:H.223, C:L.255, C:G.257 Salt bridges: 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, N.221, H.223, S.225, R.226, L.255, A.256, G.257 18 PLIP interactions: 18 interactions with chain F Hydrogen bonds: 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:T.115, F:H.116, F:N.221, F:H.223, F:L.255, F:G.257 Salt bridges: F:K.114, F:R.226 pi-Stacking: F:H.116, 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, N.221, H.223, S.225, R.226, L.255, A.256, G.257 18 PLIP interactions: 18 interactions with chain I Hydrogen bonds: 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:N.221, I:H.223, I:L.255, I:G.257 Salt bridges: I:K.114, I:R.226 pi-Stacking: I:H.116, 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, N.221, H.223, S.225, R.226, L.255, A.256, G.257 21 PLIP interactions: 21 interactions with chain L Hydrogen bonds: 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:T.115, L:H.116, L:H.116, L:N.221, L:H.223, L:S.225, L:S.225, L:L.255, L:G.257 Salt bridges: L:K.114, L:R.226 pi-Stacking: L:H.116, 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-1A chain: ADGJ
Tubulin beta-2A chain: BEHK
Kinesin-1 heavy chain: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

D
A

G
E

J
F

B
W

E
Q

H
U

K
V

C
l

F
g

I
k

L
m

Tubulin alpha-1A chain

Tubulin beta-2A chain

Kinesin-1 heavy chain

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