SMTL ID : 8vt7.1

Structure of the gamma tubulin ring complex nucleated microtubule protofilament.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

GDP.1: 15 residues within 4Å: Chain A: G.10, Q.11, C.12, Q.15, 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:S.138, A:G.141, A:G.142, A:T.143, A:G.144, A:D.177, A:D.177, A:E.181, A:E.181, A:N.204, A:N.204, A:N.226, A:N.226 pi-Stacking: A:Y.222, A:Y.222 GDP.4: 16 residues within 4Å: Chain B: L.254 Chain C: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, S.145, D.177, N.204, Y.222, N.226 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:Q.11, C:C.12, C:S.138, C:G.142, C:G.142, C:T.143, C:G.144, C:S.145, C:D.177, C:D.177, C:E.181, C:E.181, C:N.204, C:N.226, C:N.226, C:N.226 pi-Stacking: C:Y.222, C:Y.222

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

GTP.2: 23 residues within 4Å: Chain A: L.246, K.252 Chain B: G.10, Q.11, A.12, Q.15, D.104, A.105, A.106, N.107, S.146, G.149, G.150, T.151, G.152, I.177, T.185, E.189, N.212, Y.230, N.234, I.237 Ligands: MG.3 22 PLIP interactions: 19 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.11, B:A.12, B:Q.15, B:D.104, B:A.105, B:A.106, B:N.107, B:S.146, B:G.150, B:T.151, B:G.152, B:E.189, B:N.212, B:N.212, B:N.234, B:N.234 pi-Stacking: B:Y.230, B:Y.230 pi-Cation interactions: B:Y.230 Salt bridges: A:K.252, A:K.252, A:K.252 GTP.5: 22 residues within 4Å: Chain C: L.246, K.252 Chain D: G.10, Q.11, A.12, Q.15, D.104, A.105, A.106, N.107, S.146, G.149, G.150, T.151, G.152, T.185, E.189, N.212, Y.230, N.234, I.237 Ligands: MG.6 22 PLIP interactions: 19 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Q.11, D:A.12, D:Q.15, D:D.104, D:A.105, D:A.106, D:N.107, D:S.146, D:G.150, D:T.151, D:G.152, D:E.189, D:N.212, D:N.212, D:N.234, D:N.234 pi-Stacking: D:Y.230, D:Y.230 pi-Cation interactions: D:Y.230 Salt bridges: C:K.252, C:K.252, C:K.252

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: K.252 Chain B: Q.11, E.77 Ligands: GTP.2 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain C: K.252 Chain D: Q.11, E.77 Ligands: GTP.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aher, A. et al., Structure of the gamma-tubulin ring complex-capped microtubule. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-03-27

Peptides

Tubulin beta-3 chain: AC
Tubulin alpha-1B chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

C
A

B
J

D
B

Tubulin beta-3 chain

Tubulin alpha-1B chain

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