SMTL ID : 9f3s.1

13pf mosaic 20%E254Q - 80% E254N microtubule from recombinant human tubulin decorated with EB3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-6-6-mer

Ligands

12 x GTP: GUANOSINE-5'-TRIPHOSPHATE

GTP.1: 20 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, D.110, A.111, A.112, N.113, S.152, G.155, G.156, T.157, I.183, T.191, E.195, N.218, Y.236, N.240 Chain F: K.252 Ligands: MG.2 19 PLIP interactions: 17 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:Q.11, C:A.12, C:A.111, C:A.112, C:N.113, C:N.113, C:S.152, C:G.155, C:G.156, C:T.157, C:T.191, C:E.195, C:N.218, C:N.218, C:N.240, C:N.240 pi-Cation interactions: C:Y.236 Salt bridges: F:K.252, F:K.252 GTP.3: 17 residues within 4Å: Chain C: N.266 Chain D: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.141, G.142, T.143, D.177, N.204, Y.222, N.226 Ligands: MG.4 22 PLIP interactions: 21 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.11, D:C.12, D:A.97, D:G.98, D:N.99, D:N.99, D:N.99, D:S.138, D:G.141, D:G.142, D:T.143, D:G.144, D:D.177, D:D.177, D:N.204, D:N.226, D:N.226, D:N.226, C:N.266 pi-Stacking: D:Y.222, D:Y.222 pi-Cation interactions: D:Y.222 GTP.5: 21 residues within 4Å: Chain D: K.252 Chain E: G.10, Q.11, A.12, Q.15, D.110, A.111, A.112, N.113, S.152, G.155, G.156, T.157, I.183, T.191, E.195, N.218, Y.236, N.240, I.243 Ligands: MG.6 20 PLIP interactions: 18 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:Q.11, E:A.12, E:A.111, E:A.112, E:N.113, E:S.152, E:G.155, E:G.156, E:T.157, E:T.191, E:E.195, E:N.218, E:N.240, E:N.240, E:N.240 pi-Stacking: E:Y.236, E:Y.236 pi-Cation interactions: E:Y.236 Salt bridges: D:K.252, D:K.252 GTP.7: 18 residues within 4Å: Chain F: G.10, Q.11, C.12, Q.15, G.96, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 Ligands: MG.8 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:Q.11, F:C.12, F:A.97, F:G.98, F:N.99, F:S.138, F:G.141, F:G.142, F:T.143, F:G.144, F:D.177, F:D.177, F:N.204, F:N.226, F:N.226, F:N.226 pi-Stacking: F:Y.222 GTP.9: 22 residues within 4Å: Chain G: G.10, Q.11, A.12, Q.15, D.110, A.111, A.112, N.113, S.152, G.155, G.156, T.157, I.183, T.191, E.195, N.218, Y.236, L.239, N.240 Chain J: L.246, K.252 Ligands: MG.10 17 PLIP interactions: 15 interactions with chain G, 2 interactions with chain J Hydrogen bonds: G:Q.11, G:A.12, G:A.111, G:A.112, G:N.113, G:S.152, G:G.156, G:T.157, G:T.191, G:E.195, G:N.218, G:N.240, G:N.240, G:N.240 pi-Cation interactions: G:Y.236 Salt bridges: J:K.252, J:K.252 GTP.11: 19 residues within 4Å: Chain G: N.266 Chain H: G.10, Q.11, C.12, Q.15, G.96, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 Ligands: MG.12 20 PLIP interactions: 19 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:Q.11, H:C.12, H:A.97, H:G.98, H:N.99, H:N.99, H:S.138, H:G.141, H:G.142, H:T.143, H:G.144, H:D.177, H:D.177, H:N.204, H:N.226, H:N.226, H:N.226, G:N.266 pi-Stacking: H:Y.222, H:Y.222 GTP.13: 20 residues within 4Å: Chain H: K.252 Chain I: G.10, Q.11, A.12, Q.15, D.110, A.111, A.112, N.113, S.152, G.155, G.156, T.157, T.191, E.195, N.218, Y.236, N.240, I.243 Ligands: MG.14 21 PLIP interactions: 19 interactions with chain I, 2 interactions with chain H Hydrogen bonds: I:Q.11, I:A.12, I:D.110, I:A.111, I:A.112, I:N.113, I:S.152, I:G.155, I:G.156, I:T.157, I:T.191, I:E.195, I:N.218, I:N.240, I:N.240, I:N.240 pi-Stacking: I:Y.236, I:Y.236 pi-Cation interactions: I:Y.236 Salt bridges: H:K.252, H:K.252 GTP.15: 19 residues within 4Å: Chain J: G.10, Q.11, C.12, Q.15, I.16, G.96, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 Ligands: MG.16 16 PLIP interactions: 16 interactions with chain J Hydrogen bonds: J:Q.11, J:C.12, J:A.97, J:G.98, J:N.99, J:N.99, J:S.138, J:G.142, J:T.143, J:G.144, J:N.204, J:N.226, J:N.226, J:N.226 pi-Stacking: J:Y.222, J:Y.222 GTP.17: 22 residues within 4Å: Chain K: G.10, Q.11, A.12, Q.15, D.110, A.111, A.112, N.113, S.152, G.155, G.156, T.157, I.183, T.191, E.195, N.218, Y.236, N.240, I.243 Chain N: L.246, K.252 Ligands: MG.18 18 PLIP interactions: 16 interactions with chain K, 2 interactions with chain N Hydrogen bonds: K:Q.11, K:A.12, K:A.111, K:A.112, K:N.113, K:S.152, K:G.156, K:T.157, K:T.191, K:E.195, K:N.218, K:N.240, K:N.240, K:N.240 pi-Stacking: K:Y.236 pi-Cation interactions: K:Y.236 Salt bridges: N:K.252, N:K.252 GTP.19: 18 residues within 4Å: Chain K: N.266 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, D.177, N.204, Y.222, N.226 Ligands: MG.20 21 PLIP interactions: 20 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:Q.11, L:C.12, L:D.67, L:A.97, L:G.98, L:N.99, L:N.99, L:S.138, L:G.142, L:T.143, L:G.144, L:D.177, L:D.177, L:N.204, L:N.226, L:N.226, L:N.226, K:N.266 pi-Stacking: L:Y.222, L:Y.222 pi-Cation interactions: L:Y.222 GTP.21: 21 residues within 4Å: Chain L: K.252 Chain M: G.10, Q.11, A.12, Q.15, E.83, A.111, A.112, N.113, S.152, G.155, G.156, T.157, I.183, T.191, E.195, N.218, Y.236, N.240, I.243 Ligands: MG.22 21 PLIP interactions: 19 interactions with chain M, 2 interactions with chain L Hydrogen bonds: M:Q.11, M:A.12, M:A.111, M:A.112, M:N.113, M:S.152, M:G.155, M:G.156, M:T.157, M:T.191, M:E.195, M:N.218, M:Y.236, M:N.240, M:N.240, M:N.240 pi-Stacking: M:Y.236, M:Y.236 pi-Cation interactions: M:Y.236 Salt bridges: L:K.252, L:K.252 GTP.23: 19 residues within 4Å: Chain N: G.10, Q.11, C.12, Q.15, E.69, G.96, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 Ligands: MG.24 18 PLIP interactions: 18 interactions with chain N Hydrogen bonds: N:Q.11, N:C.12, N:A.97, N:G.98, N:N.99, N:N.99, N:S.138, N:G.142, N:T.143, N:G.144, N:D.177, N:D.177, N:N.204, N:N.226, N:N.226, N:N.226 pi-Stacking: N:Y.222, N:Y.222

12 x MG: MAGNESIUM ION

MG.2: 2 residues within 4Å: Chain C: E.83 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain D: E.69 Ligands: GTP.3 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.69 MG.6: 2 residues within 4Å: Chain E: E.83 Ligands: GTP.5 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain F: E.69 Ligands: GTP.7 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain H: E.69 Ligands: GTP.11 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Ligands: GTP.13 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain J: E.69 Ligands: GTP.15 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:E.69 MG.18: 2 residues within 4Å: Chain K: E.83 Ligands: GTP.17 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain L: E.69 Ligands: GTP.19 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:E.69 MG.22: 4 residues within 4Å: Chain L: K.252 Chain M: E.83, T.157 Ligands: GTP.21 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain N: E.69 Ligands: GTP.23 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:E.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Estevez-Gallego, J. et al., Hydrolysis-deficient mosaic microtubules as faithful mimics of the GTP cap. Nat Commun (2025)

Release Date

2025-03-19

Peptides

Microtubule-associated protein RP/EB family member 3: AB
Detyrosinated tubulin alpha-1B chain: CEGIKM
Tubulin beta-3 chain: DFHJLN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

B
T

C
A

E
G

G
C

I
I

K
E

M
K

D
B

F
N

H
D

J
P

L
F

N
R

Microtubule-associated protein RP/EB family member 3

Detyrosinated tubulin alpha-1B chain

Tubulin beta-3 chain

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