SMTL ID : 7sj8.1

13pf wildtype microtubule from recombinant human tubulin decorated with kinesin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

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

GTP.1: 21 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, E.77, D.104, A.105, A.106, N.107, S.146, G.149, G.150, T.151, I.177, T.185, E.189, N.212, Y.230, N.234 Chain J: L.246 Ligands: MG.2 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain J Hydrogen bonds: A:Q.11, A:A.12, A:D.104, A:A.105, A:A.106, A:N.107, A:S.146, A:G.149, A:G.150, A:T.151, A:T.151, A:T.185, A:N.212, A:N.212, A:N.234, A:N.234 pi-Stacking: A:Y.230 pi-Cation interactions: A:Y.230 Salt bridges: J:K.252 GTP.3: 21 residues within 4Å: Chain B: G.10, Q.11, A.12, Q.15, E.77, D.104, A.105, A.106, N.107, S.146, G.149, G.150, T.151, I.177, T.185, E.189, N.212, Y.230, N.234 Chain K: L.246 Ligands: MG.4 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain K Hydrogen bonds: B:Q.11, B:A.12, B:D.104, B:A.105, B:A.106, B:N.107, B:S.146, B:G.149, B:G.150, B:T.151, B:T.151, B:T.185, B:N.212, B:N.212, B:N.234, B:N.234 pi-Stacking: B:Y.230 pi-Cation interactions: B:Y.230 Salt bridges: K:K.252 GTP.5: 21 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, E.77, D.104, A.105, A.106, N.107, S.146, G.149, G.150, T.151, I.177, T.185, E.189, N.212, Y.230, N.234 Chain I: L.246 Ligands: MG.6 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain I Hydrogen bonds: C:Q.11, C:A.12, C:D.104, C:A.105, C:A.106, C:N.107, C:S.146, C:G.149, C:G.150, C:T.151, C:T.151, C:T.185, C:N.212, C:N.212, C:N.234, C:N.234 pi-Stacking: C:Y.230 pi-Cation interactions: C:Y.230 Salt bridges: I:K.252 GTP.7: 21 residues within 4Å: Chain D: G.10, Q.11, A.12, Q.15, E.77, D.104, A.105, A.106, N.107, S.146, G.149, G.150, T.151, I.177, T.185, E.189, N.212, Y.230, N.234 Chain G: L.246 Ligands: MG.8 20 PLIP interactions: 18 interactions with chain D, 2 interactions with chain G Hydrogen bonds: D:Q.11, D:A.12, D:D.104, D:A.105, D:A.106, D:N.107, D:S.146, D:G.149, D:G.150, D:T.151, D:T.151, D:T.185, D:N.212, D:N.212, D:N.234, D:N.234 pi-Stacking: D:Y.230 pi-Cation interactions: D:Y.230 Salt bridges: G:K.252, G:K.252 GTP.9: 21 residues within 4Å: Chain E: G.10, Q.11, A.12, Q.15, E.77, D.104, A.105, A.106, N.107, S.146, G.149, G.150, T.151, I.177, T.185, E.189, N.212, Y.230, N.234 Chain L: L.246 Ligands: MG.10 19 PLIP interactions: 18 interactions with chain E, 1 interactions with chain L Hydrogen bonds: E:Q.11, E:A.12, E:D.104, E:A.105, E:A.106, E:N.107, E:S.146, E:G.149, E:G.150, E:T.151, E:T.151, E:T.185, E:N.212, E:N.212, E:N.234, E:N.234 pi-Stacking: E:Y.230 pi-Cation interactions: E:Y.230 Salt bridges: L:K.252 GTP.11: 21 residues within 4Å: Chain F: G.10, Q.11, A.12, Q.15, E.77, D.104, A.105, A.106, N.107, S.146, G.149, G.150, T.151, I.177, T.185, E.189, N.212, Y.230, N.234 Chain H: L.246 Ligands: MG.12 19 PLIP interactions: 18 interactions with chain F, 1 interactions with chain H Hydrogen bonds: F:Q.11, F:A.12, F:D.104, F:A.105, F:A.106, F:N.107, F:S.146, F:G.149, F:G.150, F:T.151, F:T.151, F:T.185, F:N.212, F:N.212, F:N.234, F:N.234 pi-Stacking: F:Y.230 pi-Cation interactions: F:Y.230 Salt bridges: H:K.252

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.77 Ligands: GTP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.77 MG.4: 2 residues within 4Å: Chain B: E.77 Ligands: GTP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.77 MG.6: 2 residues within 4Å: Chain C: E.77 Ligands: GTP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.77 MG.8: 2 residues within 4Å: Chain D: E.77 Ligands: GTP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.77 MG.10: 2 residues within 4Å: Chain E: E.77 Ligands: GTP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.77 MG.12: 2 residues within 4Å: Chain F: E.77 Ligands: GTP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.77

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

GDP.13: 14 residues within 4Å: Chain G: 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 G Hydrogen bonds: 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:T.143, G:G.144, G:D.177, G:N.204, G:N.226, G:N.226, G:N.226 GDP.14: 14 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, N.226 16 PLIP interactions: 16 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:T.143, H:G.144, H:D.177, H:N.204, H:N.226, H:N.226, H:N.226 GDP.15: 14 residues within 4Å: Chain I: 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 I Hydrogen bonds: I:Q.11, I:C.12, I:S.138, I:G.141, I:G.142, I:T.143, I:T.143, I:T.143, I:T.143, I:G.144, I:D.177, I:N.204, I:N.226, I:N.226, I:N.226 GDP.16: 14 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, N.226 15 PLIP interactions: 15 interactions with chain J Hydrogen bonds: 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:T.143, J:G.144, J:D.177, J:N.204, J:N.226, J:N.226, J:N.226 GDP.17: 14 residues within 4Å: Chain K: 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 K Hydrogen bonds: K:Q.11, K:C.12, K:S.138, K:G.141, K:G.142, K:T.143, K:T.143, K:T.143, K:T.143, K:G.144, K:D.177, K:N.204, K:N.226, K:N.226, K:N.226 GDP.18: 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 15 PLIP interactions: 15 interactions with chain L Hydrogen bonds: 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:T.143, L:G.144, L:D.177, L:N.204, L:N.226, L:N.226, L:N.226

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: ABCDEF
Tubulin beta-3 chain: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
J

E
K

F
L

G
F

H
D

I
G

J
H

K
I

L
B

Tubulin alpha-1B chain

Tubulin beta-3 chain

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