SMTL ID : 5n5n.1

Cryo-EM structure of tsA201 cell alpha1B and betaI and betaIVb microtubules

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.20 Å

Oligo State

hetero-6-6-mer

Ligands

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

G2P.1: 18 residues within 4Å: Chain A: G.10, Q.11, C.12, Q.15, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, L.225, N.226 Chain C: E.254 Ligands: MG.2 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Q.11, A:Q.11, A:C.12, A:G.98, A:N.99, A:S.138, A:G.142, A:T.143, A:T.143, A:G.144, A:N.204, A:N.226, A:N.226, A:N.226, C:E.254, C:E.254 pi-Stacking: A:Y.222, A:Y.222 G2P.15: 16 residues within 4Å: Chain H: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, L.225, N.226 Ligands: MG.16 17 PLIP interactions: 17 interactions with chain H Hydrogen bonds: H:Q.11, H:Q.11, H:Q.11, H:C.12, H:G.98, H:N.99, H:S.138, H:G.142, H:T.143, H:T.143, H:G.144, H:N.204, H:N.226, H:N.226, H:N.226 pi-Stacking: H:Y.222, H:Y.222 G2P.17: 16 residues within 4Å: Chain I: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, L.225, N.226 Ligands: MG.18 17 PLIP interactions: 17 interactions with chain I Hydrogen bonds: I:Q.11, I:Q.11, I:Q.11, I:C.12, I:G.98, I:N.99, I:S.138, I:G.142, I:T.143, I:T.143, I:G.144, I:N.204, I:N.226, I:N.226, I:N.226 pi-Stacking: I:Y.222, I:Y.222 G2P.19: 18 residues within 4Å: Chain D: E.254 Chain J: G.10, Q.11, C.12, Q.15, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, L.225, N.226 Ligands: MG.20 18 PLIP interactions: 16 interactions with chain J, 2 interactions with chain D Hydrogen bonds: J:Q.11, J:Q.11, J:C.12, J:G.98, J:N.99, J:S.138, J:G.142, J:T.143, J:T.143, J:G.144, J:N.204, J:N.226, J:N.226, J:N.226, D:E.254, D:E.254 pi-Stacking: J:Y.222, J:Y.222 G2P.21: 17 residues within 4Å: Chain G: E.254 Chain K: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, L.225, N.226 Ligands: MG.22 18 PLIP interactions: 16 interactions with chain K, 2 interactions with chain G Hydrogen bonds: K:Q.11, K:Q.11, K:C.12, K:G.98, K:N.99, K:S.138, K:G.142, K:T.143, K:T.143, K:G.144, K:N.204, K:N.226, K:N.226, K:N.226, G:E.254, G:E.254 pi-Stacking: K:Y.222, K:Y.222 G2P.23: 16 residues within 4Å: Chain L: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, L.225, N.226 Ligands: MG.24 17 PLIP interactions: 17 interactions with chain L Hydrogen bonds: L:Q.11, L:Q.11, L:Q.11, L:C.12, L:N.99, L:S.138, L:G.141, L:G.142, L:T.143, L:T.143, L:G.144, L:N.204, L:N.226, L:N.226, L:N.226 pi-Stacking: L:Y.222, L:Y.222

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Q.11, D.67, T.143 Ligands: G2P.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: Q.11, E.71 Ligands: GTP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: Q.11, E.71 Ligands: GTP.5 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain D: Q.11, E.71 Ligands: GTP.7 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain E: Q.11, E.71 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain F: Q.11, E.71 Ligands: GTP.11 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain G: Q.11 Ligands: GTP.13 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain H: Q.11, D.67, T.143 Ligands: G2P.15 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain I: Q.11, D.67, T.143 Ligands: G2P.17 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain J: Q.11, D.67, T.143 Ligands: G2P.19 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain K: Q.11, D.67, T.143 Ligands: G2P.21 No protein-ligand interaction detected (PLIP) MG.24: 4 residues within 4Å: Chain L: Q.11, D.67, T.143 Ligands: G2P.23 No protein-ligand interaction detected (PLIP)

6 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.3: 22 residues within 4Å: Chain A: K.252 Chain B: G.10, Q.11, A.12, Q.15, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, L.227, N.228 Ligands: MG.4 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.11, B:Q.11, B:A.12, B:D.98, B:A.99, B:A.100, B:N.101, B:S.140, B:G.144, B:T.145, B:T.145, B:G.146, B:E.183, B:N.206, B:N.206, B:Y.224, B:N.228 pi-Stacking: B:Y.224, B:Y.224 Salt bridges: A:K.252, A:K.252 GTP.5: 22 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, L.227, N.228 Chain H: K.252 Ligands: MG.6 21 PLIP interactions: 19 interactions with chain C, 2 interactions with chain H Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:D.98, C:A.99, C:A.100, C:N.101, C:S.140, C:G.144, C:T.145, C:T.145, C:G.146, C:E.183, C:N.206, C:N.206, C:Y.224, C:N.228 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: H:K.252, H:K.252 GTP.7: 21 residues within 4Å: Chain D: G.10, Q.11, A.12, Q.15, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, L.227, N.228 Chain I: K.252 Ligands: MG.8 20 PLIP interactions: 18 interactions with chain D, 2 interactions with chain I Hydrogen bonds: D:Q.11, D:Q.11, D:A.12, D:D.98, D:A.99, D:A.100, D:N.101, D:S.140, D:G.144, D:T.145, D:G.146, D:E.183, D:N.206, D:N.206, D:Y.224, D:N.228 pi-Stacking: D:Y.224, D:Y.224 Salt bridges: I:K.252, I:K.252 GTP.9: 21 residues within 4Å: Chain E: G.10, Q.11, A.12, Q.15, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, L.227, N.228 Chain J: K.252 Ligands: MG.10 20 PLIP interactions: 18 interactions with chain E, 2 interactions with chain J Hydrogen bonds: E:Q.11, E:Q.11, E:A.12, E:D.98, E:A.99, E:A.100, E:N.101, E:S.140, E:G.144, E:T.145, E:G.146, E:E.183, E:N.206, E:N.206, E:Y.224, E:N.228 pi-Stacking: E:Y.224, E:Y.224 Salt bridges: J:K.252, J:K.252 GTP.11: 22 residues within 4Å: Chain F: G.10, Q.11, A.12, Q.15, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, L.227, N.228 Chain K: K.252 Ligands: MG.12 21 PLIP interactions: 19 interactions with chain F, 2 interactions with chain K Hydrogen bonds: F:Q.11, F:Q.11, F:A.12, F:D.98, F:A.99, F:A.100, F:N.101, F:S.140, F:G.144, F:T.145, F:T.145, F:G.146, F:E.183, F:N.206, F:N.206, F:Y.224, F:N.228 pi-Stacking: F:Y.224, F:Y.224 Salt bridges: K:K.252, K:K.252 GTP.13: 22 residues within 4Å: Chain G: G.10, Q.11, A.12, Q.15, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, L.227, N.228 Chain L: K.252 Ligands: MG.14 20 PLIP interactions: 18 interactions with chain G, 2 interactions with chain L Hydrogen bonds: G:Q.11, G:Q.11, G:A.12, G:D.98, G:A.99, G:A.100, G:N.101, G:S.140, G:G.144, G:T.145, G:G.146, G:E.183, G:N.206, G:N.206, G:Y.224, G:N.228 pi-Stacking: G:Y.224, G:Y.224 Salt bridges: L:K.252, L:K.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vemu, A. et al., Tubulin isoform composition tunes microtubule dynamics. Mol. Biol. Cell (2017)

Release Date

2017-11-01

Peptides

Tubulin beta chain: AHIJKL
Tubulin alpha-1B chain: BCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

H
A

I
C

J
D

K
E

L
F

B
K

C
G

D
H

E
I

F
J

G
L

Tubulin beta chain

Tubulin alpha-1B chain

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