SMTL ID : 5ucy.1 (1 other biounit)

Cryo-EM map of protofilament of microtubule doublet

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

GTP.1: 24 residues within 4Å: Chain A: G.10, Q.11, G.12, G.13, Q.15, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, T.179, N.206, Y.224, L.227, N.228 Chain B: K.252 Ligands: MG.2 29 PLIP interactions: 25 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.10, A:G.10, A:Q.11, A:G.12, A:G.13, A:E.71, A:A.99, A:A.100, A:N.101, A:N.101, A:N.101, A:S.140, A:G.142, A:G.143, A:G.144, A:T.145, A:G.146, A:T.179, A:T.179, A:N.206, A:Y.224, A:N.228, A:N.228, B:Q.245 pi-Stacking: A:Y.224 pi-Cation interactions: A:Y.224 Salt bridges: B:K.252, B:K.252, B:K.252 GTP.4: 24 residues within 4Å: Chain C: G.10, Q.11, G.12, G.13, Q.15, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, T.179, N.206, Y.224, L.227, N.228 Chain D: K.252 Ligands: MG.5 28 PLIP interactions: 25 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:G.10, C:G.10, C:Q.11, C:G.12, C:G.13, C:E.71, C:A.99, C:A.100, C:N.101, C:N.101, C:N.101, C:S.140, C:G.142, C:G.143, C:G.144, C:T.145, C:G.146, C:T.179, C:T.179, C:N.206, C:Y.224, C:N.228, C:N.228 pi-Stacking: C:Y.224 pi-Cation interactions: C:Y.224 Salt bridges: D:K.252, D:K.252, D:K.252 GTP.7: 24 residues within 4Å: Chain E: G.10, Q.11, G.12, G.13, Q.15, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, T.179, N.206, Y.224, L.227, N.228 Chain F: K.252 Ligands: MG.8 28 PLIP interactions: 25 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:G.10, E:G.10, E:Q.11, E:G.12, E:G.13, E:E.71, E:A.99, E:A.100, E:N.101, E:N.101, E:N.101, E:S.140, E:G.142, E:G.143, E:G.144, E:T.145, E:G.146, E:T.179, E:T.179, E:N.206, E:Y.224, E:N.228, E:N.228 pi-Stacking: E:Y.224 pi-Cation interactions: E:Y.224 Salt bridges: F:K.252, F:K.252, F:K.252

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: D.69, L.70, E.71, D.98, T.145 Chain B: K.252 Ligands: GTP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.69, A:E.71, A:E.71 MG.5: 7 residues within 4Å: Chain C: D.69, L.70, E.71, D.98, T.145 Chain D: K.252 Ligands: GTP.4 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.69, C:E.71, C:E.71 MG.8: 7 residues within 4Å: Chain E: D.69, L.70, E.71, D.98, T.145 Chain F: K.252 Ligands: GTP.7 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.69, E:E.71, E:E.71

3 x GDP: GUANOSINE-5'-DIPHOSPHATE(Covalent)

GDP.3: 19 residues within 4Å: Chain B: G.10, Q.11, C.12, G.13, Q.15, N.99, S.138, G.142, T.143, G.144, S.145, V.169, D.203, N.204, L.207, Y.222, L.225, N.226 Chain E: L.248 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.10, 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:G.144, B:N.204, B:Y.222, B:Y.222, B:N.226, B:N.226 pi-Stacking: B:Y.222 GDP.6: 19 residues within 4Å: Chain A: L.248 Chain D: G.10, Q.11, C.12, G.13, Q.15, N.99, S.138, G.142, T.143, G.144, S.145, V.169, D.203, N.204, L.207, Y.222, L.225, N.226 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:G.10, D:Q.11, D:Q.11, D:C.12, D:N.99, D:S.138, D:G.142, D:T.143, D:T.143, D:T.143, D:G.144, D:N.204, D:Y.222, D:Y.222, D:N.226, D:N.226 pi-Stacking: D:Y.222 GDP.9: 18 residues within 4Å: Chain F: G.10, Q.11, C.12, G.13, Q.15, N.99, S.138, G.142, T.143, G.144, S.145, V.169, D.203, N.204, L.207, Y.222, L.225, N.226 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:G.10, F:Q.11, F:Q.11, F:C.12, F:N.99, F:S.138, F:G.142, F:T.143, F:T.143, F:T.143, F:G.144, F:N.204, F:Y.222, F:Y.222, F:N.226, F:N.226 pi-Stacking: F:Y.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ichikawa, M. et al., Subnanometre-resolution structure of the doublet microtubule reveals new classes of microtubule-associated proteins. Nat Commun (2017)

Release Date

2017-05-10

Peptides

Tubulin alpha chain: ACE
Tubulin beta chain: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Tubulin alpha chain

Tubulin beta chain

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