SMTL ID : 6evz.1

Cryo-EM structure of GDP-microtubule co-polymerised with doublecortin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

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

GDP.1: 14 residues within 4Å: Chain A: Q.11, C.12, Q.15, A.97, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 Chain H: L.248 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.11, A:Q.11, A:C.12, A:S.138, A:G.142, A:T.143, A:T.143, A:T.143, A:G.144, A:D.177, A:N.204, A:N.204, A:N.226, A:N.226 GDP.2: 14 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, A.97, 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.3: 14 residues within 4Å: Chain C: 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 Chain J: L.248 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:Q.11, C:Q.11, C:C.12, C:S.138, C:G.142, C:T.143, C:T.143, C:T.143, C:G.144, C:D.177, C:N.204, C:N.204, C:N.226, C:N.226 GDP.4: 13 residues within 4Å: Chain D: 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 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:S.138, D:G.141, D:G.142, D:T.143, D:T.143, D:T.143, D:G.144, D:D.177, D:N.204, D:N.204, D:N.226, D:N.226 GDP.7: 15 residues within 4Å: Chain E: L.248 Chain F: G.10, Q.11, C.12, Q.15, A.97, 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 F Hydrogen bonds: F:Q.11, F:Q.11, F:C.12, F:S.138, F:G.142, F:T.143, F:T.143, F:T.143, F:G.144, F:D.177, F:N.204, F:N.204, F:N.226, F:N.226 GDP.8: 14 residues within 4Å: Chain G: G.10, Q.11, C.12, Q.15, A.97, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:Q.11, G:Q.11, G:C.12, G:S.138, G:G.141, G:G.142, G:T.143, G:T.143, G:T.143, G:G.144, G:D.177, G:N.204, G:N.204, G:N.226, G:N.226

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

GTP.5: 22 residues within 4Å: Chain E: 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 17 PLIP interactions: 16 interactions with chain E, 1 interactions with chain G 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.143, 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: G:K.252 GTP.9: 23 residues within 4Å: Chain B: L.246 Chain H: 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.10 17 PLIP interactions: 16 interactions with chain H, 1 interactions with chain B Hydrogen bonds: H:Q.11, H:Q.11, H:A.12, H:A.99, H:A.100, H:N.101, H:S.140, H:G.143, H:G.144, H:T.145, H:G.146, H:E.183, H:N.206, H:N.228, H:N.228 pi-Cation interactions: H:Y.224 Salt bridges: B:K.252 GTP.11: 23 residues within 4Å: Chain A: L.246 Chain I: 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.12 17 PLIP interactions: 16 interactions with chain I, 1 interactions with chain A Hydrogen bonds: I:Q.11, I:Q.11, I:A.12, I:A.99, I:A.100, I:N.101, I:S.140, I:G.143, I:G.144, I:T.145, I:G.146, I:E.183, I:N.206, I:N.228, I:N.228 pi-Cation interactions: I:Y.224 Salt bridges: A:K.252 GTP.13: 22 residues within 4Å: Chain J: 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.14 17 PLIP interactions: 16 interactions with chain J, 1 interactions with chain D Hydrogen bonds: J:Q.11, J:Q.11, J:A.12, J:A.99, J:A.100, J:N.101, J:S.140, J:G.143, J:G.144, J:T.145, J:G.146, J:E.183, J:N.206, J:N.228, J:N.228 pi-Cation interactions: J:Y.224 Salt bridges: D:K.252 GTP.15: 22 residues within 4Å: Chain K: 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.16 19 PLIP interactions: 1 interactions with chain C, 18 interactions with chain K Salt bridges: C:K.252 Hydrogen bonds: K:Q.11, K:Q.11, K:A.12, K:D.69, K:D.98, K:A.99, K:A.100, K:N.101, K:S.140, K:G.143, K:G.144, K:T.145, K:G.146, K:E.183, K:N.206, K:N.228, K:N.228 pi-Cation interactions: K:Y.224 GTP.17: 23 residues within 4Å: Chain F: L.246 Chain L: 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.18 17 PLIP interactions: 15 interactions with chain L, 2 interactions with chain F Hydrogen bonds: L:Q.11, L:Q.11, L:A.12, L:A.99, L:A.100, L:N.101, L:S.140, L:G.144, L:T.145, L:G.146, L:E.183, L:N.206, L:N.228, L:N.228 pi-Cation interactions: L:Y.224 Salt bridges: F:K.252, F:K.252

6 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain E: Q.11, E.71 Ligands: GTP.5 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain H: Q.11, E.71 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain I: Q.11, E.71 Ligands: GTP.11 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain J: Q.11, E.71 Ligands: GTP.13 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain K: Q.11, E.71 Ligands: GTP.15 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain L: Q.11, E.71 Ligands: GTP.17 No protein-ligand interaction detected (PLIP)

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 beta chain: ABCDFG
Tubulin alpha-1B chain: EHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
D

D
I

F
B

G
H

E
A

H
E

I
J

J
C

K
L

L
K

Tubulin beta chain

Tubulin alpha-1B chain

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