SMTL ID : 6rf8.1

Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to 13-protofilament GDP-microtubule

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-2-mer

Ligands

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

GDP.1: 13 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 Chain E: L.239 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:G.142, B:T.143, B:T.143, B:G.144, B:D.177, B:N.204, B:N.204, B:N.204, B:N.226 GDP.4: 13 residues within 4Å: Chain C: L.239 Chain D: G.10, Q.11, C.12, Q.15, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:G.142, D:T.143, D:T.143, D:G.144, D:D.177, D:N.204, D:N.204, D:N.204, D:N.226

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

GTP.2: 17 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, E.62, D.89, A.91, S.131, G.134, G.135, T.136, I.162, N.197, Y.215, N.219, I.222 Ligands: MG.3 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:Q.11, C:A.12, C:E.62, C:A.91, C:N.92, C:S.131, C:G.134, C:G.135, C:T.136, C:T.170, C:T.170, C:N.197, C:N.197, C:N.219, C:N.219 GTP.5: 17 residues within 4Å: Chain E: G.10, Q.11, A.12, Q.15, E.62, D.89, A.91, S.131, G.134, G.135, T.136, I.162, N.197, Y.215, N.219, I.222 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:Q.11, E:A.12, E:E.62, E:A.91, E:N.92, E:S.131, E:G.134, E:G.135, E:T.136, E:T.170, E:T.170, E:N.197, E:N.197, E:N.219, E:N.219

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain C: Q.11, E.62 Ligands: GTP.2 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain E: Q.11, E.62 Ligands: GTP.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cook, A.D. et al., A microtubule RELION-based pipeline for cryo-EM image processing. J.Struct.Biol. (2020)

Release Date

2020-04-15

Peptides

Neuronal migration protein doublecortin: A
Tubulin beta-2B chain: BD
Tubulin alpha-1B chain: CE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
N

B
b

D
B

C
A

E
a

Neuronal migration protein doublecortin

Tubulin beta-2B chain

Tubulin alpha-1B chain

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