SMTL ID : 6evy.1

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

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, I.16, E.71, 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 Chain H: L.246 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:A.99, A:A.100, A:N.101, A:N.101, A:S.140, A:G.143, A:G.144, A:T.145, A:T.145, A:G.146, A:E.183, A:N.206, A:N.228, A:N.228 GTP.4: 24 residues within 4Å: Chain B: L.246 Chain C: G.10, Q.11, A.12, Q.15, I.16, 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.5 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:A.99, C:A.100, C:N.101, C:S.140, C:G.143, C:G.144, C:T.145, C:G.146, C:E.183, C:N.206, C:N.228, C:N.228 Salt bridges: B:K.252 GTP.6: 23 residues within 4Å: Chain D: G.10, Q.11, A.12, Q.15, I.16, E.71, 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 Chain J: L.246 Ligands: MG.7 18 PLIP interactions: 17 interactions with chain D, 1 interactions with chain J Hydrogen bonds: D:Q.11, D:Q.11, D:A.12, D:A.99, D:A.100, D:N.101, D:N.101, D:S.140, D:G.143, D:G.144, D:T.145, D:T.145, D:G.146, D:E.183, D:N.206, D:N.228, D:N.228 Salt bridges: J:K.252 GTP.8: 24 residues within 4Å: Chain E: G.10, Q.11, A.12, Q.15, I.16, 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 Chain I: L.246 Ligands: MG.9 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.143, E:G.144, E:T.145, E:G.146, E:E.183, E:N.206, E:N.228, E:N.228 Salt bridges: I:K.252 GTP.10: 24 residues within 4Å: Chain F: G.10, Q.11, A.12, Q.15, I.16, 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 Chain L: L.246 Ligands: MG.11 17 PLIP interactions: 16 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:N.101, F:S.140, F:G.143, F:G.144, F:T.145, F:G.146, F:E.183, F:N.206, F:N.228, F:N.228 Salt bridges: L:K.252 GTP.12: 23 residues within 4Å: Chain G: Q.11, A.12, Q.15, I.16, E.71, 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 Chain K: L.246, K.252 Ligands: MG.13 16 PLIP interactions: 15 interactions with chain G, 1 interactions with chain K Hydrogen bonds: G:Q.11, G:A.12, G:A.99, G:A.100, G:N.101, G:N.101, G:S.140, G:G.144, G:T.145, G:T.145, G:G.146, G:E.183, G:N.206, G:N.228, G:N.228 Salt bridges: 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 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.71 MG.5: 3 residues within 4Å: Chain C: Q.11, E.71 Ligands: GTP.4 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.71 MG.7: 3 residues within 4Å: Chain D: Q.11, E.71 Ligands: GTP.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.71 MG.9: 3 residues within 4Å: Chain E: Q.11, E.71 Ligands: GTP.8 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.71 MG.11: 3 residues within 4Å: Chain F: Q.11, E.71 Ligands: GTP.10 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.71 MG.13: 3 residues within 4Å: Chain G: Q.11, E.71 Ligands: GTP.12 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.71

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

GSP.3: 17 residues within 4Å: Chain A: L.248, E.254 Chain B: G.10, Q.11, C.12, Q.15, E.69, A.97, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 12 PLIP interactions: 12 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:G.144, B:N.204, B:N.204, B:N.226, B:N.226 GSP.14: 15 residues within 4Å: Chain H: G.10, Q.11, C.12, Q.15, E.69, A.97, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:Q.11, H:Q.11, H:C.12, H:E.69, H:S.138, H:G.142, H:T.143, H:T.143, H:G.144, H:N.204, H:N.204, H:N.226, H:N.226 GSP.15: 17 residues within 4Å: Chain D: L.248, E.254 Chain I: G.10, Q.11, C.12, Q.15, E.69, A.97, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: 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:N.204, I:N.204, I:N.226, I:N.226 GSP.16: 15 residues within 4Å: Chain J: G.10, Q.11, C.12, Q.15, E.69, A.97, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 12 PLIP interactions: 12 interactions with chain J Hydrogen bonds: J:Q.11, J:C.12, J:E.69, J:S.138, J:G.142, J:T.143, J:T.143, J:G.144, J:N.204, J:N.204, J:N.226, J:N.226 GSP.17: 17 residues within 4Å: Chain F: L.248, E.254 Chain K: G.10, Q.11, C.12, Q.15, E.69, A.97, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 13 PLIP interactions: 13 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:N.204, K:N.204, K:N.226, K:N.226 GSP.18: 15 residues within 4Å: Chain L: G.10, Q.11, C.12, Q.15, E.69, A.97, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 13 PLIP interactions: 13 interactions with chain L Hydrogen bonds: L:Q.11, L:Q.11, L:C.12, L:E.69, L:S.138, L:G.142, L:T.143, L:T.143, L:G.144, L:N.204, L:N.204, L:N.226, L:N.226

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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