SMTL ID : 3jaw.1

Atomic model of a microtubule seam based on a cryo-EM reconstruction of the EB3-bound microtubule (merged dataset containing tubulin bound to GTPgammaS, GMPCPP, and GDP)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.90 Å

Oligo State

hetero-2-2-mer

Ligands

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

GTP.1: 23 residues within 4Å: Chain A: 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, T.179, E.183, N.206, Y.224, N.228, I.231 Chain B: L.246, K.252 Ligands: MG.2 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.11, A:A.12, A:Q.15, A:A.99, A:A.100, A:N.101, A:S.140, A:G.144, A:T.145, A:T.145, A:G.146, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252, B:K.252 GTP.4: 21 residues within 4Å: Chain C: 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, N.228, I.231 Ligands: MG.5 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:Q.11, C:A.12, C:Q.15, C:A.99, C:A.100, C:N.101, C:S.140, C:G.144, C:T.145, C:T.145, C:G.146, C:E.183, C:N.206, C:N.206, C:N.228, C:N.228 pi-Stacking: C:Y.224, C:Y.224

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Q.11, E.71 Chain B: K.252 Ligands: GTP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.71 MG.5: 2 residues within 4Å: Chain C: E.71 Ligands: GTP.4 No protein-ligand interaction detected (PLIP)

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

GSP.3: 17 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, E.69, A.97, N.99, S.138, G.141, G.142, T.143, G.144, V.169, D.177, N.204, Y.222, N.226 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:Q.15, B:E.69, B:N.99, B:S.138, B:G.142, B:T.143, B:G.144, B:D.177, B:N.204, B:N.226, B:N.226, B:N.226 pi-Stacking: B:Y.222 GSP.6: 17 residues within 4Å: Chain C: L.248, E.254 Chain D: G.10, Q.11, C.12, D.67, E.69, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:E.69, D:S.138, D:G.142, D:T.143, D:G.144, D:D.177, D:N.204, D:N.204, D:N.226, D:N.226 pi-Stacking: D:Y.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, R. et al., Mechanistic Origin of Microtubule Dynamic Instability and Its Modulation by EB Proteins. Cell(Cambridge,Mass.) (2015)

Release Date

2015-08-12

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Tubulin alpha-1B chain

Tubulin beta chain

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