SMTL ID : 9dkx.1

CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

3 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 15 residues within 4Å: Chain A: P.1514, M.1515, V.1516, H.1518, S.1545, R.1546, T.1547, G.1548, K.1549, T.1550, I.1551, C.1675, W.1703, R.1780, R.2295 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:V.1516, A:H.1518, A:R.1546, A:R.1546, A:T.1547, A:G.1548, A:K.1549, A:T.1550, A:T.1550, A:T.1550, A:I.1551, A:R.1780, A:R.1780 Salt bridges: A:K.1549, A:R.2295, A:R.2295 pi-Stacking: A:W.1703 ADP.2: 16 residues within 4Å: Chain A: L.552, I.553, T.555, L.558, A.581, G.582, T.583, G.584, K.585, T.586, E.587, I.712, L.753, R.754, K.757 Ligands: MG.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:I.553, A:I.553, A:G.582, A:T.583, A:G.584, A:K.585, A:T.586, A:T.586, A:R.754, A:K.757 Salt bridges: A:K.585, A:R.754 ADP.3: 17 residues within 4Å: Chain A: I.1175, T.1177, T.1180, P.1202, P.1203, G.1204, S.1205, G.1206, K.1207, T.1208, M.1209, I.1353, Y.1354, P.1402, R.1403, T.1406 Ligands: MG.7 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:I.1175, A:T.1180, A:T.1180, A:S.1205, A:G.1206, A:K.1207, A:T.1208, A:M.1209 Salt bridges: A:K.1207, A:R.1403, A:R.1403

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.4: 20 residues within 4Å: Chain A: F.830, S.831, F.836, K.858, A.859, G.860, G.862, K.863, T.864, A.865, D.938, E.978, C.1003, S.1007, K.1008, H.1011, E.1068, R.1332, R.1335 Ligands: MG.6 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.831, A:S.831, A:G.860, A:G.862, A:K.863, A:T.864, A:A.865, A:H.1011, A:E.1068 Salt bridges: A:K.863, A:R.1332, A:R.1335, A:R.1335, A:R.1335

3 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: T.586 Ligands: ADP.2 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain A: T.864, D.938, E.978, R.1332 Ligands: ATP.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.864, A:D.938, A:E.978 MG.7: 3 residues within 4Å: Chain A: K.1207, E.1271 Ligands: ADP.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kendrick, A.A. et al., Multiple steps of dynein activation by Lis1 visualized by cryo-EM. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-06-04

Peptides

Dynein heavy chain, cytoplasmic: A
Nuclear distribution protein PAC1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Dynein heavy chain, cytoplasmic

Nuclear distribution protein PAC1

Related Entries With Identical Sequence