SMTL ID : 7sja.1

Undecorated 13pf E254N microtubule from recombinant human tubulin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

12 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Covalent)

GTP.1: 22 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, D.75, E.77, D.104, A.105, A.106, N.107, S.146, G.149, G.150, T.151, G.152, I.177, T.185, N.212, Y.230, N.234 Chain H: K.252 Ligands: MG.2 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain H Hydrogen bonds: A:Q.11, A:A.12, A:D.75, A:E.77, A:A.105, A:N.107, A:S.146, A:G.149, A:G.150, A:T.151, A:T.151, A:G.152, A:T.185, A:N.212, A:N.234, A:N.234 pi-Stacking: A:Y.230, A:Y.230 Salt bridges: H:K.252, H:K.252 GTP.3: 21 residues within 4Å: Chain A: N.260 Chain B: G.10, Q.11, C.12, Q.15, D.67, 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.4 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:E.69, B:A.97, B:N.99, B:N.99, B:S.138, B:G.141, B:G.142, B:T.143, B:T.143, B:G.144, B:D.177, B:N.204, B:N.204, B:N.226, B:N.226, A:N.260 pi-Stacking: B:Y.222, B:Y.222 GTP.5: 22 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, D.75, E.77, D.104, A.105, A.106, N.107, S.146, G.149, G.150, T.151, G.152, I.177, T.185, N.212, Y.230, N.234 Chain I: K.252 Ligands: MG.6 20 PLIP interactions: 18 interactions with chain C, 2 interactions with chain I Hydrogen bonds: C:Q.11, C:A.12, C:D.75, C:E.77, C:A.105, C:N.107, C:S.146, C:G.149, C:G.150, C:T.151, C:T.151, C:G.152, C:T.185, C:N.212, C:N.234, C:N.234 pi-Stacking: C:Y.230, C:Y.230 Salt bridges: I:K.252, I:K.252 GTP.7: 21 residues within 4Å: Chain C: N.260 Chain D: G.10, Q.11, C.12, Q.15, D.67, 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.8 21 PLIP interactions: 20 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:E.69, D:A.97, D:N.99, D:N.99, D:S.138, D:G.141, D:G.142, D:T.143, D:T.143, D:G.144, D:D.177, D:N.204, D:N.204, D:N.226, D:N.226, C:N.260 pi-Stacking: D:Y.222, D:Y.222 GTP.9: 22 residues within 4Å: Chain E: G.10, Q.11, A.12, Q.15, D.75, E.77, D.104, A.105, A.106, N.107, S.146, G.149, G.150, T.151, G.152, I.177, T.185, N.212, Y.230, N.234 Chain G: K.252 Ligands: MG.10 20 PLIP interactions: 18 interactions with chain E, 2 interactions with chain G Hydrogen bonds: E:Q.11, E:A.12, E:D.75, E:E.77, E:A.105, E:N.107, E:S.146, E:G.149, E:G.150, E:T.151, E:T.151, E:G.152, E:T.185, E:N.212, E:N.234, E:N.234 pi-Stacking: E:Y.230, E:Y.230 Salt bridges: G:K.252, G:K.252 GTP.11: 21 residues within 4Å: Chain E: N.260 Chain F: G.10, Q.11, C.12, Q.15, D.67, 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.12 21 PLIP interactions: 20 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:Q.11, F:Q.11, F:C.12, F:E.69, F:A.97, F:N.99, F:N.99, F:S.138, F:G.141, F:G.142, F:T.143, F:T.143, F:G.144, F:D.177, F:N.204, F:N.204, F:N.226, F:N.226, E:N.260 pi-Stacking: F:Y.222, F:Y.222 GTP.13: 20 residues within 4Å: Chain G: G.10, Q.11, C.12, Q.15, D.67, 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.14 20 PLIP interactions: 20 interactions with chain G Hydrogen bonds: G:Q.11, G:Q.11, G:C.12, G:E.69, G:A.97, G:N.99, G:N.99, G:S.138, G:G.141, G:G.142, G:T.143, G:T.143, G:G.144, G:D.177, G:N.204, G:N.204, G:N.226, G:N.226 pi-Stacking: G:Y.222, G:Y.222 GTP.15: 20 residues within 4Å: Chain H: G.10, Q.11, C.12, Q.15, D.67, 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.16 20 PLIP interactions: 20 interactions with chain H Hydrogen bonds: H:Q.11, H:Q.11, H:C.12, H:E.69, H:A.97, H:N.99, 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:N.204, H:N.204, H:N.226, H:N.226 pi-Stacking: H:Y.222, H:Y.222 GTP.17: 20 residues within 4Å: Chain I: G.10, Q.11, C.12, Q.15, D.67, 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.18 20 PLIP interactions: 20 interactions with chain I Hydrogen bonds: I:Q.11, I:Q.11, I:C.12, I:E.69, I:A.97, I:N.99, I:N.99, I:S.138, I:G.141, I:G.142, I:T.143, I:T.143, I:G.144, I:D.177, I:N.204, I:N.204, I:N.226, I:N.226 pi-Stacking: I:Y.222, I:Y.222 GTP.19: 22 residues within 4Å: Chain F: K.252 Chain J: G.10, Q.11, A.12, Q.15, D.75, E.77, D.104, A.105, A.106, N.107, S.146, G.149, G.150, T.151, G.152, I.177, T.185, N.212, Y.230, N.234 Ligands: MG.20 20 PLIP interactions: 18 interactions with chain J, 2 interactions with chain F Hydrogen bonds: J:Q.11, J:A.12, J:D.75, J:E.77, J:A.105, J:N.107, J:S.146, J:G.149, J:G.150, J:T.151, J:T.151, J:G.152, J:T.185, J:N.212, J:N.234, J:N.234 pi-Stacking: J:Y.230, J:Y.230 Salt bridges: F:K.252, F:K.252 GTP.21: 22 residues within 4Å: Chain B: K.252 Chain K: G.10, Q.11, A.12, Q.15, D.75, E.77, D.104, A.105, A.106, N.107, S.146, G.149, G.150, T.151, G.152, I.177, T.185, N.212, Y.230, N.234 Ligands: MG.22 21 PLIP interactions: 18 interactions with chain K, 3 interactions with chain B Hydrogen bonds: K:Q.11, K:A.12, K:D.75, K:E.77, K:A.105, K:N.107, K:S.146, K:G.149, K:G.150, K:T.151, K:T.151, K:G.152, K:T.185, K:N.212, K:N.234, K:N.234 pi-Stacking: K:Y.230, K:Y.230 Salt bridges: B:K.252, B:K.252, B:K.252 GTP.23: 22 residues within 4Å: Chain D: K.252 Chain L: G.10, Q.11, A.12, Q.15, D.75, E.77, D.104, A.105, A.106, N.107, S.146, G.149, G.150, T.151, G.152, I.177, T.185, N.212, Y.230, N.234 Ligands: MG.24 20 PLIP interactions: 18 interactions with chain L, 2 interactions with chain D Hydrogen bonds: L:Q.11, L:A.12, L:D.75, L:E.77, L:A.105, L:N.107, L:S.146, L:G.149, L:G.150, L:T.151, L:T.151, L:G.152, L:T.185, L:N.212, L:N.234, L:N.234 pi-Stacking: L:Y.230, L:Y.230 Salt bridges: D:K.252, D:K.252

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: E.77, D.104, T.151 Chain H: K.252 Ligands: GTP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.77, A:D.104 MG.4: 3 residues within 4Å: Chain B: E.69, T.143 Ligands: GTP.3 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain C: E.77, D.104, T.151 Chain I: K.252 Ligands: GTP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.77, C:D.104 MG.8: 3 residues within 4Å: Chain D: E.69, T.143 Ligands: GTP.7 No protein-ligand interaction detected (PLIP) MG.10: 5 residues within 4Å: Chain E: E.77, D.104, T.151 Chain G: K.252 Ligands: GTP.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.77, E:D.104 MG.12: 3 residues within 4Å: Chain F: E.69, T.143 Ligands: GTP.11 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain G: E.69, T.143 Ligands: GTP.13 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain H: E.69, T.143 Ligands: GTP.15 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain I: E.69, T.143 Ligands: GTP.17 No protein-ligand interaction detected (PLIP) MG.20: 5 residues within 4Å: Chain F: K.252 Chain J: E.77, D.104, T.151 Ligands: GTP.19 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:E.77, J:D.104 MG.22: 5 residues within 4Å: Chain B: K.252 Chain K: E.77, D.104, T.151 Ligands: GTP.21 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:E.77, K:D.104 MG.24: 5 residues within 4Å: Chain D: K.252 Chain L: E.77, D.104, T.151 Ligands: GTP.23 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:E.77, L:D.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

LaFrance, B.J. et al., Structural transitions in the GTP cap visualized by cryo-electron microscopy of catalytically inactive microtubules. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-01-19

Peptides

Tubulin alpha-1B chain: ACEJKL
Tubulin beta-3 chain: BDFGHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

J
J

K
K

L
L

B
B

D
D

F
F

G
G

H
H

I
I

Tubulin alpha-1B chain

Tubulin beta-3 chain

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