SMTL ID : 8v2i.1

Structure of alpha1B and betaI/IVb microtubule bound to GMPCPP

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

GTP.1: 22 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, L.227, N.228 Chain B: K.252 Ligands: MG.2 25 PLIP interactions: 23 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:A.99, A:A.100, A:N.101, A:N.101, A:S.140, A:G.143, A:G.144, A:T.145, A:G.146, A:T.179, A:T.179, A:E.183, A:N.206, A:N.206, A:Y.224, A:N.228, A:N.228 pi-Stacking: A:Y.224, A:Y.224 pi-Cation interactions: A:Y.224 Salt bridges: B:K.252, B:K.252 GTP.5: 22 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, N.228 Chain D: K.252 Ligands: MG.6 21 PLIP interactions: 19 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:A.99, C:A.100, C:N.101, C:N.101, C:S.140, C:G.144, C:T.145, C:G.146, C:E.183, C:N.206, C:N.206, C:Y.224, C:N.228, C:N.228 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252, D:K.252

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.69, D.98, T.145 Chain B: K.252 Ligands: GTP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.98, A:D.98 MG.4: 2 residues within 4Å: Chain B: E.69 Ligands: G2P.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.69 MG.6: 3 residues within 4Å: Chain C: D.69, E.71 Ligands: GTP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.71 MG.8: 2 residues within 4Å: Chain D: E.69 Ligands: G2P.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.69

2 x G2P: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

G2P.3: 19 residues within 4Å: Chain B: 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.4 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:G.96, B:N.99, B:S.138, B:G.142, B:T.143, B:T.143, B:G.144, B:D.177, B:N.204, B:N.204, B:Y.222, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222 G2P.7: 20 residues within 4Å: Chain A: E.254 Chain D: 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.8 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:G.98, D:S.138, D:G.142, D:T.143, D:T.143, D:G.144, D:D.177, D:N.204, D:N.204, D:Y.222, D:N.226, D:N.226 pi-Stacking: D:Y.222, D:Y.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zehr, E.A. et al., Cryo-EM structures of human a1B/bI+bIVb microtubules shed light on isoform specific assembly. Biorxiv (2023)

Release Date

2023-12-13

Peptides

Tubulin alpha-1B chain: AC
Tubulin beta chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
I

B
B

D
Q

Tubulin alpha-1B chain

Tubulin beta chain

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