SMTL ID : 8v2j.1

Structure of alpha1B and betaI/IVb microtubule bound to GDP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

GDP.1: 18 residues within 4Å: Chain A: G.10, Q.11, C.12, Q.15, I.16, E.69, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, N.226 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:Q.11, A:Q.11, A:C.12, A:N.99, A:S.138, A:G.142, A:T.143, A:T.143, A:T.143, A:G.144, A:D.177, A:E.181, A:N.204, A:N.226, A:N.226, A:N.226 pi-Stacking: A:Y.222, A:Y.222 GDP.2: 17 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, E.69, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:N.99, B:S.138, B:G.142, B:T.143, B:T.143, B:T.143, B:G.144, B:D.177, B:N.204, B:Y.222, B:N.226, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222

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

GTP.3: 25 residues within 4Å: Chain A: L.246, K.252 Chain C: G.10, Q.11, A.12, Q.15, E.71, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, T.179, N.206, Y.224, L.227, N.228, I.231 Ligands: MG.4 20 PLIP interactions: 18 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:D.98, C:A.99, C:N.101, C:S.140, C:G.144, C:T.145, C:G.146, C:T.179, C:T.179, C:N.206, C:N.228, C:N.228, C:N.228 pi-Stacking: C:Y.224 pi-Cation interactions: C:Y.224 Salt bridges: A:K.252, A:K.252 GTP.5: 25 residues within 4Å: Chain B: L.246, K.252 Chain D: G.10, Q.11, A.12, Q.15, I.16, E.71, D.98, A.99, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, N.228, I.231 Ligands: MG.6 21 PLIP interactions: 2 interactions with chain B, 19 interactions with chain D Salt bridges: B:K.252, B:K.252 Hydrogen bonds: D:Q.11, D:A.12, D:D.98, D:D.98, D:A.99, D:N.101, D:S.140, D:G.144, D:T.145, D:G.146, D:E.183, D:N.206, D:Y.224, D:N.228, D:N.228, D:N.228 pi-Stacking: D:Y.224, D:Y.224 pi-Cation interactions: D:Y.224

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: K.252 Chain C: Q.11, E.71, D.98 Ligands: GTP.3 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.71 MG.6: 6 residues within 4Å: Chain B: K.252 Chain D: Q.11, D.69, E.71, D.98 Ligands: GTP.5 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zehr, E.A. et al., Cryo-EM structures of human a1B/bI+bIVb and a1A/bIII microtubules show tubulin tails link tubulin dimers and shed light on isoform specific assembly. To be published

Release Date

2024-11-27

Peptides

Tubulin beta chain: AB
Tubulin alpha-1B chain: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
E

C
A

D
D

Tubulin beta chain

Tubulin alpha-1B chain

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