SMTL ID : 6evw.1

Cryo-EM structure of GMPCPP-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: 22 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, 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, Y.224, N.228 Ligands: MG.2 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain I Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:D.98, 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:G.146, A:T.179, A:T.179, A:E.183, A:N.206, A:N.228, A:N.228, A:N.228 Salt bridges: I:K.252 GTP.3: 23 residues within 4Å: Chain B: G.10, Q.11, A.12, Q.15, I.16, 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 Ligands: MG.4 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain H Hydrogen bonds: B:Q.11, B:Q.11, B:A.12, B:D.98, B:A.99, B:A.100, B:N.101, B:N.101, B:S.140, B:G.143, B:G.144, B:T.145, B:G.146, B:T.179, B:N.228, B:N.228, B:N.228 Salt bridges: H:K.252 GTP.5: 22 residues within 4Å: 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.142, G.143, G.144, T.145, G.146, I.171, T.179, E.183, Y.224, N.228 Ligands: MG.6 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain K Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:D.98, C:A.99, C:A.100, C:N.101, C:N.101, C:S.140, C:G.143, C:G.144, C:T.145, C:G.146, C:E.183, C:N.228, C:N.228, C:N.228 Salt bridges: K:K.252 GTP.7: 23 residues within 4Å: Chain D: G.10, Q.11, A.12, Q.15, I.16, 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 Ligands: MG.8 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:D.98, 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:G.146, D:T.179, D:N.228, D:N.228, D:N.228 Salt bridges: J:K.252 GTP.9: 23 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.142, G.143, G.144, T.145, G.146, I.171, T.179, E.183, Y.224, N.228 Chain L: K.252 Ligands: MG.10 18 PLIP interactions: 17 interactions with chain E, 1 interactions with chain L Hydrogen bonds: E:Q.11, E:Q.11, E:A.12, E:D.98, E:A.99, E:A.100, E:N.101, E:N.101, E:S.140, E:G.143, E:G.144, E:T.145, E:G.146, E:E.183, E:N.228, E:N.228, E:N.228 Salt bridges: L:K.252 GTP.11: 22 residues within 4Å: Chain F: G.10, Q.11, A.12, Q.15, I.16, E.71, D.98, 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 Ligands: MG.12 18 PLIP interactions: 17 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:Q.11, F:Q.11, F:A.12, F:D.98, 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:T.179, F:N.228, F:N.228, F:N.228 Salt bridges: G:K.252

12 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.4: 3 residues within 4Å: Chain B: Q.11, E.71 Ligands: GTP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.71 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 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.71 MG.14: 3 residues within 4Å: Chain G: Q.11, E.69 Ligands: G2P.13 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain H: Q.11, E.69 Ligands: G2P.15 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain I: Q.11, E.69 Ligands: G2P.17 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain J: Q.11, E.69 Ligands: G2P.19 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain K: Q.11, E.69 Ligands: G2P.21 No protein-ligand interaction detected (PLIP) MG.24: 3 residues within 4Å: Chain L: Q.11, E.69 Ligands: G2P.23 No protein-ligand interaction detected (PLIP)

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

G2P.13: 19 residues within 4Å: Chain E: E.254 Chain G: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, T.178, N.204, Y.222, N.226 Ligands: MG.14 17 PLIP interactions: 15 interactions with chain G, 2 interactions with chain E Hydrogen bonds: G:Q.11, G:C.12, G:A.97, G:G.98, G:N.99, G:S.138, G:G.141, G:G.142, G:T.143, G:G.144, G:D.177, G:T.178, G:N.204, G:N.226, G:N.226, E:E.254, E:E.254 G2P.15: 20 residues within 4Å: Chain A: E.254 Chain H: G.10, Q.11, C.12, Q.15, E.69, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, T.178, N.204, Y.222, N.226 Ligands: MG.16 20 PLIP interactions: 18 interactions with chain H, 2 interactions with chain A Hydrogen bonds: H:Q.11, H:Q.11, H:C.12, H:A.97, H:G.98, H:N.99, H:S.138, H:G.141, H:G.142, H:T.143, H:T.143, H:G.144, H:D.177, H:T.178, H:T.178, H:N.204, H:N.226, H:N.226, A:E.254, A:E.254 G2P.17: 19 residues within 4Å: Chain I: G.10, Q.11, C.12, Q.15, E.69, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, T.178, N.204, Y.222, N.226 Ligands: MG.18 15 PLIP interactions: 15 interactions with chain I Hydrogen bonds: I:Q.11, I:C.12, I:A.97, I:G.98, I:N.99, I:S.138, I:G.141, I:G.142, I:T.143, I:G.144, I:D.177, I:T.178, I:N.204, I:N.226, I:N.226 G2P.19: 19 residues within 4Å: Chain C: E.254 Chain J: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, T.178, N.204, Y.222, N.226 Ligands: MG.20 19 PLIP interactions: 17 interactions with chain J, 2 interactions with chain C Hydrogen bonds: J:Q.11, J:Q.11, J:C.12, J:A.97, J:G.98, J:N.99, J:S.138, J:G.141, J:G.142, J:T.143, J:G.144, J:D.177, J:T.178, J:T.178, J:N.204, J:N.226, J:N.226, C:E.254, C:E.254 G2P.21: 19 residues within 4Å: Chain K: G.10, Q.11, C.12, Q.15, E.69, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, T.178, N.204, Y.222, N.226 Ligands: MG.22 16 PLIP interactions: 16 interactions with chain K Hydrogen bonds: K:Q.11, K:C.12, K:A.97, K:G.98, K:N.99, K:S.138, K:G.141, K:G.142, K:T.143, K:G.144, K:D.177, K:T.178, K:T.178, K:N.204, K:N.226, K:N.226 G2P.23: 19 residues within 4Å: Chain L: G.10, Q.11, C.12, Q.15, E.69, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, T.178, N.204, Y.222, N.226 Ligands: MG.24 16 PLIP interactions: 16 interactions with chain L Hydrogen bonds: L:Q.11, L:C.12, L:A.97, L:G.98, L:N.99, L:S.138, L:G.141, L:G.142, L:T.143, L:G.144, L:D.177, L:T.178, L:T.178, 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: ABCDEF
Tubulin beta chain: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
J

C
C

D
L

E
A

F
K

G
B

H
F

I
G

J
D

K
I

L
H

Tubulin alpha-1B chain

Tubulin beta chain

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