SMTL ID : 6evx.1

Cryo-EM structure of GDP.Pi-microtubule rapidly 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: 15 residues within 4Å: Chain A: 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 H: L.248 Ligands: PO4.13 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.11, A:Q.11, A:C.12, A:S.138, A:G.141, A:G.142, A:T.143, A:T.143, A:T.143, A:G.144, A:N.204, A:N.204, A:N.226, A:N.226 GDP.6: 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 Ligands: PO4.5 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:Q.11, C:Q.11, C:C.12, C:S.138, C:G.141, C:G.142, C:T.143, C:T.143, C:T.143, C:G.144, C:N.204, C:N.204, C:N.226, C:N.226 GDP.7: 15 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 Chain J: L.248 Ligands: PO4.18 14 PLIP interactions: 14 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:N.204, D:N.204, D:N.226, D:N.226 GDP.9: 13 residues within 4Å: Chain E: G.10, Q.11, C.12, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 Ligands: PO4.8 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:Q.11, E:Q.11, E:C.12, E:S.138, E:G.141, E:G.142, E:T.143, E:T.143, E:T.143, E:G.144, E:N.204, E:N.204, E:N.226, E:N.226 GDP.10: 15 residues within 4Å: Chain B: L.248 Chain F: 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 Ligands: PO4.4 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:Q.11, F:Q.11, F:C.12, F:S.138, F:G.141, F:G.142, F:T.143, F:T.143, F:T.143, F:G.144, F:N.204, F:N.204, F:N.226, F:N.226 GDP.12: 14 residues within 4Å: Chain G: 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 Ligands: PO4.11 14 PLIP interactions: 14 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:N.204, G:N.204, G:N.226, G:N.226

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

GTP.2: 21 residues within 4Å: Chain B: G.10, Q.11, A.12, Q.15, E.71, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, T.179, N.206, Y.224, N.228, I.231 Chain G: L.246, K.252 Ligands: MG.3 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain G Hydrogen bonds: B:Q.11, B:Q.11, B:A.12, B:A.99, B:A.100, B:N.101, B:S.140, B:G.143, B:G.144, B:T.145, B:T.145, B:G.146, B:T.179, B:T.179, B:N.206, B:Y.224, B:Y.224, B:N.228, B:N.228, B:N.228 Salt bridges: G:K.252 GTP.14: 20 residues within 4Å: Chain C: K.252 Chain H: G.10, Q.11, A.12, Q.15, E.71, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, T.179, N.206, Y.224, N.228, I.231 Ligands: MG.15 20 PLIP interactions: 20 interactions with chain H 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:T.145, H:G.146, H:T.179, H:T.179, H:N.206, H:Y.224, H:Y.224, H:N.228, H:N.228, H:N.228 GTP.16: 20 residues within 4Å: Chain A: K.252 Chain I: G.10, Q.11, A.12, Q.15, E.71, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, T.179, N.206, Y.224, N.228, I.231 Ligands: MG.17 21 PLIP interactions: 20 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:T.145, I:G.146, I:T.179, I:T.179, I:N.206, I:Y.224, I:Y.224, I:N.228, I:N.228, I:N.228 Salt bridges: A:K.252 GTP.19: 21 residues within 4Å: Chain E: L.246, K.252 Chain J: G.10, Q.11, A.12, Q.15, E.71, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, T.179, N.206, Y.224, N.228, I.231 Ligands: MG.20 21 PLIP interactions: 20 interactions with chain J, 1 interactions with chain E 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:T.145, J:G.146, J:T.179, J:T.179, J:N.206, J:Y.224, J:Y.224, J:N.228, J:N.228, J:N.228 Salt bridges: E:K.252 GTP.21: 20 residues within 4Å: Chain D: K.252 Chain K: G.10, Q.11, A.12, Q.15, E.71, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, T.179, N.206, Y.224, N.228, I.231 Ligands: MG.22 21 PLIP interactions: 20 interactions with chain K, 1 interactions with chain D Hydrogen bonds: K:Q.11, K:Q.11, K:A.12, K:A.99, K:A.100, K:N.101, K:S.140, K:G.143, K:G.144, K:T.145, K:T.145, K:G.146, K:T.179, K:T.179, K:N.206, K:Y.224, K:Y.224, K:N.228, K:N.228, K:N.228 Salt bridges: D:K.252 GTP.23: 20 residues within 4Å: Chain F: K.252 Chain L: G.10, Q.11, A.12, Q.15, E.71, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, T.179, N.206, Y.224, N.228, I.231 Ligands: MG.24 21 PLIP interactions: 20 interactions with chain L, 1 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.143, L:G.144, L:T.145, L:T.145, L:G.146, L:T.179, L:T.179, L:N.206, L:Y.224, L:Y.224, L:N.228, L:N.228, L:N.228 Salt bridges: F:K.252

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain B: Q.11, E.71 Ligands: GTP.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.71 MG.15: 3 residues within 4Å: Chain H: Q.11, E.71 Ligands: GTP.14 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.71 MG.17: 3 residues within 4Å: Chain I: Q.11, E.71 Ligands: GTP.16 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:E.71 MG.20: 3 residues within 4Å: Chain J: Q.11, E.71 Ligands: GTP.19 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:E.71 MG.22: 3 residues within 4Å: Chain K: Q.11, E.71 Ligands: GTP.21 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:E.71 MG.24: 3 residues within 4Å: Chain L: Q.11, E.71 Ligands: GTP.23 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:E.71

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 8 residues within 4Å: Chain B: D.251, E.254 Chain F: Q.11, E.69, A.97, N.99, T.143 Ligands: GDP.10 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.69, F:N.99, F:T.143 PO4.5: 5 residues within 4Å: Chain C: Q.11, E.69, A.97, T.143 Ligands: GDP.6 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.69 PO4.8: 6 residues within 4Å: Chain E: Q.11, E.69, A.97, N.99, T.143 Ligands: GDP.9 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.69, E:N.99 PO4.11: 5 residues within 4Å: Chain G: Q.11, E.69, A.97, T.143 Ligands: GDP.12 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:E.69, G:E.69 PO4.13: 7 residues within 4Å: Chain A: Q.11, E.69, A.97, T.143 Chain H: D.251, E.254 Ligands: GDP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.11 PO4.18: 7 residues within 4Å: Chain D: Q.11, E.69, N.99, T.143 Chain J: D.251, E.254 Ligands: GDP.7 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.69, D:N.99, D:T.143

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

2018-07-11

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

C
G

D
D

E
I

F
B

G
H

B
A

H
E

I
J

J
C

K
L

L
K

Tubulin beta chain

Tubulin alpha-1B chain

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