SMTL ID : 5ucy.2 (1 other biounit)

Cryo-EM map of protofilament of microtubule doublet

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 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

1 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

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

GDP.3: 18 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 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

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: A
Tubulin beta chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tubulin alpha chain

Tubulin beta chain

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