SMTL ID : 6rfd.1

Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to 14-protofilament GDP-microtubule

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-mer

Ligands

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

GTP.1: 17 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, E.62, D.89, S.131, G.134, G.135, T.136, T.170, E.174, N.197, Y.215, N.219, I.222 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.11, A:A.12, A:E.62, A:S.131, A:G.134, A:G.135, A:T.136, A:T.136, A:T.170, A:E.174, A:N.197, A:N.219, A:N.219, A:N.219 GTP.3: 17 residues within 4Å: Chain B: G.10, Q.11, A.12, Q.15, E.62, D.89, S.131, G.134, G.135, T.136, T.170, E.174, N.197, Y.215, N.219, I.222 Ligands: MG.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Q.11, B:A.12, B:E.62, B:S.131, B:G.134, B:G.135, B:T.136, B:T.136, B:T.170, B:E.174, B:N.197, B:N.219, B:N.219, B:N.219

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: G.10, Q.11 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: G.10, Q.11 Ligands: GTP.3 No protein-ligand interaction detected (PLIP)

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

GDP.5: 13 residues within 4Å: Chain A: L.239, E.245 Chain C: G.10, Q.11, C.12, Q.15, G.141, G.142, T.143, D.177, N.204, Y.222, N.226 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.11, C:Q.11, C:C.12, C:G.142, C:T.143, C:T.143, C:D.177, C:N.204, C:N.204, C:N.226, C:N.226, A:E.245 GDP.6: 13 residues within 4Å: Chain B: L.239, E.245 Chain D: G.10, Q.11, C.12, Q.15, G.141, G.142, T.143, D.177, N.204, Y.222, N.226 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:G.142, D:T.143, D:T.143, D:D.177, D:N.204, D:N.204, D:N.226, D:N.226, B:E.245

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manka, S.W. et al., Pseudo-repeats in doublecortin make distinct mechanistic contributions to microtubule regulation. Embo Rep. (2020)

Release Date

2020-05-13

Peptides

Tubulin alpha-1B chain: AB
Tubulin beta-2B chain: CD
Neuronal migration protein doublecortin: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
a

C
B

D
b

E
N

Tubulin alpha-1B chain

Tubulin beta-2B chain

Neuronal migration protein doublecortin

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