SMTL ID : 6ew0.1

Cryo-EM structure of GDP-microtubule co-polymerised with doublecortin and supplemented with Taxol

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

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

GTP.1: 23 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, E.183, N.206, Y.224, N.228, I.231 Chain H: K.252 Ligands: MG.2 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain H Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:A.99, A:A.100, A:N.101, A:S.140, A:G.144, A:T.145, A:G.146, A:E.183, A:N.206, A:N.228, A:N.228 pi-Cation interactions: A:Y.224 Salt bridges: H:K.252 GTP.5: 25 residues within 4Å: Chain B: Q.245, L.246, K.252 Chain C: G.10, Q.11, A.12, Q.15, E.71, 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, N.228, I.231 Ligands: MG.6 18 PLIP interactions: 2 interactions with chain B, 16 interactions with chain C Salt bridges: B:K.252, B:K.252 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:G.146, C:E.183, C:N.206, C:N.228, C:N.228 pi-Cation interactions: C:Y.224 GTP.7: 23 residues within 4Å: Chain D: G.10, Q.11, A.12, Q.15, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, E.183, N.206, Y.224, N.228, I.231 Chain J: K.252 Ligands: MG.8 16 PLIP interactions: 1 interactions with chain J, 15 interactions with chain D Salt bridges: J:K.252 Hydrogen bonds: D:Q.11, D:Q.11, D:A.12, 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.228, D:N.228 pi-Cation interactions: D:Y.224 GTP.9: 22 residues within 4Å: Chain E: G.10, Q.11, A.12, Q.15, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, E.183, N.206, Y.224, N.228, I.231 Ligands: MG.10 16 PLIP interactions: 15 interactions with chain E, 1 interactions with chain I Hydrogen bonds: E:Q.11, E:Q.11, E:A.12, 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.228, E:N.228 pi-Cation interactions: E:Y.224 Salt bridges: I:K.252 GTP.11: 22 residues within 4Å: Chain F: G.10, Q.11, A.12, Q.15, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, E.183, N.206, Y.224, N.228, I.231 Ligands: MG.12 16 PLIP interactions: 15 interactions with chain F, 1 interactions with chain L Hydrogen bonds: F:Q.11, F:Q.11, F:A.12, F:A.99, F:A.100, F:N.101, F:S.140, F:G.144, F:T.145, F:G.146, F:E.183, F:N.206, F:N.228, F:N.228 pi-Cation interactions: F:Y.224 Salt bridges: L:K.252 GTP.13: 25 residues within 4Å: Chain G: G.10, Q.11, A.12, Q.15, E.71, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, N.228, I.231 Chain K: L.246, K.252 Ligands: MG.14 17 PLIP interactions: 15 interactions with chain G, 2 interactions with chain K Hydrogen bonds: G:Q.11, G:Q.11, G:A.12, 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.228, G:N.228 pi-Cation interactions: G:Y.224 Salt bridges: K:K.252, K:K.252

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: Q.11, E.71 Ligands: GTP.1 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: 4 residues within 4Å: Chain E: Q.11, D.69, E.71 Ligands: GTP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.71 MG.12: 3 residues within 4Å: Chain F: Q.11, E.71 Ligands: GTP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.71 MG.14: 3 residues within 4Å: Chain G: Q.11, E.71 Ligands: GTP.13 No protein-ligand interaction detected (PLIP)

6 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.3: 14 residues within 4Å: Chain A: L.248 Chain B: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:S.138, B:G.142, B:T.143, B:T.143, B:T.143, B:G.144, B:D.177, B:N.204, B:N.204, B:N.226, B:N.226 GDP.16: 13 residues within 4Å: Chain H: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:Q.11, H:Q.11, H:C.12, H:S.138, H:G.142, H:T.143, H:T.143, H:T.143, H:G.144, H:D.177, H:N.204, H:N.204, H:N.226, H:N.226 GDP.18: 14 residues within 4Å: Chain D: L.248 Chain I: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 14 PLIP interactions: 14 interactions with chain I Hydrogen bonds: I:Q.11, I:Q.11, I:C.12, I:S.138, I:G.142, I:T.143, I:T.143, I:T.143, I:G.144, I:D.177, I:N.204, I:N.204, I:N.226, I:N.226 GDP.20: 13 residues within 4Å: Chain J: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 14 PLIP interactions: 14 interactions with chain J Hydrogen bonds: J:Q.11, J:Q.11, J:C.12, J:S.138, J:G.142, J:T.143, J:T.143, J:T.143, J:G.144, J:D.177, J:N.204, J:N.204, J:N.226, J:N.226 GDP.22: 14 residues within 4Å: Chain F: L.248 Chain K: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 14 PLIP interactions: 14 interactions with chain K Hydrogen bonds: K:Q.11, K:Q.11, K:C.12, K:S.138, K:G.142, K:T.143, K:T.143, K:T.143, K:G.144, K:D.177, K:N.204, K:N.204, K:N.226, K:N.226 GDP.24: 13 residues within 4Å: Chain L: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 14 PLIP interactions: 14 interactions with chain L Hydrogen bonds: L:Q.11, L:Q.11, L:C.12, L:S.138, L:G.142, L:T.143, L:T.143, L:T.143, L:G.144, L:D.177, L:N.204, L:N.204, L:N.226, L:N.226

6 x TA1: TAXOL(Non-covalent)

TA1.4: 18 residues within 4Å: Chain B: V.23, D.26, E.27, L.215, L.217, D.224, H.227, L.228, A.231, S.234, L.273, T.274, S.275, R.276, Q.279, P.358, R.359, L.361 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.23, B:L.215, B:L.217, B:D.224, B:L.228, B:A.231, B:P.358 Hydrogen bonds: B:T.274, B:Q.279, B:R.359, B:R.359 Salt bridges: B:R.276 TA1.15: 22 residues within 4Å: Chain H: V.23, D.26, E.27, L.215, L.217, D.224, H.227, L.228, A.231, S.234, F.270, P.272, L.273, T.274, S.275, R.276, Q.279, R.318, P.358, R.359, G.360, L.361 13 PLIP interactions: 13 interactions with chain H Hydrophobic interactions: H:V.23, H:L.215, H:L.217, H:L.228, H:A.231, H:F.270, H:P.358, H:P.358 Hydrogen bonds: H:T.274, H:Q.279, H:R.359, H:R.359 Salt bridges: H:R.276 TA1.17: 21 residues within 4Å: Chain I: V.23, D.26, E.27, L.215, L.217, D.224, H.227, L.228, A.231, S.234, P.272, L.273, T.274, S.275, R.276, Q.279, R.318, P.358, R.359, G.360, L.361 12 PLIP interactions: 12 interactions with chain I Hydrophobic interactions: I:V.23, I:L.215, I:L.217, I:L.228, I:A.231, I:P.358, I:P.358 Hydrogen bonds: I:T.274, I:Q.279, I:R.359, I:R.359 Salt bridges: I:R.276 TA1.19: 21 residues within 4Å: Chain J: V.23, D.26, E.27, L.215, L.217, D.224, H.227, L.228, A.231, S.234, P.272, L.273, T.274, S.275, R.276, Q.279, R.318, P.358, R.359, G.360, L.361 12 PLIP interactions: 12 interactions with chain J Hydrophobic interactions: J:V.23, J:L.215, J:L.217, J:L.228, J:A.231, J:P.358, J:P.358 Hydrogen bonds: J:T.274, J:Q.279, J:R.359, J:R.359 Salt bridges: J:R.276 TA1.21: 21 residues within 4Å: Chain K: V.23, D.26, E.27, L.215, L.217, D.224, H.227, L.228, A.231, S.234, P.272, L.273, T.274, S.275, R.276, Q.279, R.318, P.358, R.359, G.360, L.361 12 PLIP interactions: 12 interactions with chain K Hydrophobic interactions: K:V.23, K:L.215, K:L.217, K:L.228, K:A.231, K:P.358, K:P.358 Hydrogen bonds: K:T.274, K:Q.279, K:R.359, K:R.359 Salt bridges: K:R.276 TA1.23: 21 residues within 4Å: Chain L: V.23, D.26, E.27, L.215, L.217, D.224, H.227, L.228, A.231, S.234, P.272, L.273, T.274, S.275, R.276, Q.279, R.318, P.358, R.359, G.360, L.361 12 PLIP interactions: 12 interactions with chain L Hydrophobic interactions: L:V.23, L:L.215, L:L.217, L:L.228, L:A.231, L:P.358, L:P.358 Hydrogen bonds: L:T.274, L:Q.279, L:R.359, L:R.359 Salt bridges: L:R.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manka, S.W. et al., The role of tubulin-tubulin lattice contacts in the mechanism of microtubule dynamic instability. Nat. Struct. Mol. Biol. (2018)

Release Date

2018-07-04

Peptides

Tubulin alpha-1B chain: ACDEFG
Tubulin beta chain: BHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

C
J

D
C

E
L

F
A

G
K

B
F

H
G

I
D

J
I

K
B

L
H

Tubulin alpha-1B chain

Tubulin beta chain

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