SMTL ID : 6e88.1

Cryo-EM structure of C. elegans GDP-microtubule

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

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

GTP.1: 13 residues within 4Å: Chain A: Q.11, Q.15, E.69, D.96, A.97, A.98, N.99, S.138, E.181, N.204, Y.222 Chain B: Q.245, K.252 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:D.96, A:D.96, A:A.97, A:A.98, A:N.99, A:S.138, A:E.181, A:N.204 pi-Cation interactions: A:Y.222 Salt bridges: B:K.252, B:K.252, B:K.252 GTP.3: 18 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, L.68, D.96, A.97, A.98, N.99, S.138, G.140, G.141, G.142, T.143, G.144, E.181, N.204, Y.222 13 PLIP interactions: 1 interactions with chain D, 12 interactions with chain C Salt bridges: D:K.252 Hydrogen bonds: C:Q.11, C:A.12, C:D.96, C:A.98, C:N.99, C:S.138, C:G.142, C:T.143, C:G.144, C:E.181, C:N.204 pi-Cation interactions: C:Y.222 GTP.5: 15 residues within 4Å: Chain E: G.10, Q.11, A.12, Q.15, D.96, A.97, A.98, N.99, S.138, G.141, G.142, T.143, E.181, Y.222, N.226 16 PLIP interactions: 13 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:Q.11, E:A.12, E:D.96, E:A.98, E:N.99, E:S.138, E:G.142, E:T.143, E:E.181, E:N.204, E:N.226 pi-Stacking: E:Y.222 pi-Cation interactions: E:Y.222 Salt bridges: F:K.252, F:K.252, F:K.252 GTP.7: 16 residues within 4Å: Chain G: G.10, Q.11, A.12, Q.15, D.96, A.97, A.98, N.99, S.138, G.141, G.142, T.143, G.144, E.181, Y.222 Chain H: Q.245 12 PLIP interactions: 11 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:Q.11, G:A.12, G:D.96, G:A.97, G:N.99, G:S.138, G:G.142, G:T.143, G:G.144, G:E.181 pi-Cation interactions: G:Y.222 Salt bridges: H:K.252 GTP.9: 17 residues within 4Å: Chain I: G.10, Q.11, A.12, Q.15, D.96, A.97, A.98, N.99, S.138, G.141, G.142, T.143, G.144, T.177, E.181, Y.222 Chain J: K.252 16 PLIP interactions: 15 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:Q.11, I:A.12, I:D.96, I:D.96, I:A.97, I:A.98, I:N.99, I:S.138, I:G.142, I:T.143, I:G.144, I:E.181, I:N.226 pi-Stacking: I:Y.222 pi-Cation interactions: I:Y.222 Salt bridges: J:K.252 GTP.11: 15 residues within 4Å: Chain K: G.10, Q.11, A.12, Q.15, E.69, D.96, A.97, A.98, N.99, S.138, E.181, N.204, Y.222 Chain L: Q.245, K.252 14 PLIP interactions: 11 interactions with chain K, 3 interactions with chain L Hydrogen bonds: K:Q.11, K:D.96, K:D.96, K:A.97, K:A.98, K:N.99, K:S.138, K:G.142, K:E.181, K:N.204 pi-Cation interactions: K:Y.222 Salt bridges: L:K.252, L:K.252, L:K.252

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

GDP.2: 14 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, N.99, 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.141, B:G.142, B:T.143, B:T.143, B:T.143, B:G.144, B:D.177, B:N.204, B:N.226 pi-Cation interactions: B:Y.222 GDP.4: 14 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, N.99, 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.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 pi-Cation interactions: D:Y.222 GDP.6: 16 residues within 4Å: Chain F: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, L.225, N.226 Chain G: L.246 13 PLIP interactions: 13 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:G.144, F:N.204, F:Y.222, F:N.226 pi-Cation interactions: F:Y.222 GDP.8: 15 residues within 4Å: Chain H: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, L.225, N.226 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:Q.11, H:Q.11, H:C.12, H:S.138, H:G.141, H:G.142, H:T.143, H:T.143, H:T.143, H:G.144, H:D.177, H:N.204, H:Y.222, H:N.226 pi-Cation interactions: H:Y.222 GDP.10: 16 residues within 4Å: Chain J: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, L.225, N.226 Chain K: L.246 14 PLIP interactions: 14 interactions with chain J Hydrogen bonds: J:Q.11, J:Q.11, J:C.12, J:S.138, J:G.141, J:G.142, J:T.143, J:T.143, J:T.143, J:G.144, J:D.177, J:N.204, J:N.226 pi-Cation interactions: J:Y.222 GDP.12: 14 residues within 4Å: Chain L: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 16 PLIP interactions: 16 interactions with chain L Hydrogen bonds: L:Q.11, L:Q.11, L:C.12, L:S.138, L:G.141, L:G.142, L:T.143, L:T.143, L:T.143, L:G.144, L:D.177, L:N.204, L:N.226, L:N.226, L:N.226 pi-Cation interactions: L:Y.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaaban, S. et al., The Structure and Dynamics of C. elegans Tubulin Reveals the Mechanistic Basis of Microtubule Growth. Dev. Cell (2018)

Release Date

2018-10-10

Peptides

Tubulin alpha-2 chain: ACEGIK
Tubulin beta-2 chain: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
H

G
L

I
I

K
M

B
B

D
D

F
J

H
N

J
K

L
O

Tubulin alpha-2 chain

Tubulin beta-2 chain