SMTL ID : 9dkd.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

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

ATP.1: 19 residues within 4Å: Chain A: F.830, S.831, F.836, A.859, G.860, C.861, G.862, K.863, T.864, A.865, E.978, C.1003, S.1007, K.1008, H.1011, R.1290, E.1294, R.1332, R.1335 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:S.831, A:S.831, A:G.860, A:C.861, A:G.862, A:K.863, A:T.864, A:T.864, A:A.865, A:E.978, A:E.978, A:H.1011, A:E.1294 Salt bridges: A:K.863, A:K.863, A:R.1290, A:R.1332, A:R.1335, A:R.1335, A:R.1335 pi-Stacking: A:F.830

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

ADP.2: 13 residues within 4Å: Chain A: L.552, I.553, G.582, G.584, K.585, T.586, E.587, D.631, E.632, I.712, L.753, R.754, K.757 16 PLIP interactions: 16 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:E.587, A:E.632, A:E.632, A:R.754, A:R.754, A:K.757 Salt bridges: A:K.585, A:R.754 ADP.3: 16 residues within 4Å: Chain A: V.1513, P.1514, M.1515, V.1516, A.1544, S.1545, R.1546, T.1547, G.1548, K.1549, T.1550, I.1551, T.1673, W.1703, R.1780, R.2295 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:V.1516, A:H.1518, A:R.1546, A:T.1547, A:G.1548, A:K.1549, 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 ADP.4: 15 residues within 4Å: Chain A: I.1175, T.1180, P.1203, G.1204, G.1206, K.1207, T.1208, M.1209, I.1353, Y.1357, P.1402, R.1403, T.1406, P.1689 Ligands: MG.5 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:I.1175, A:I.1175, A:G.1204, A:G.1206, A:K.1207, A:T.1208, A:T.1208, A:M.1209, A:Y.1357, A:T.1406 Salt bridges: A:K.1207, A:R.1403, A:R.1403

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: T.1208, D.1270 Ligands: ADP.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.1208, A:D.1270

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dynein heavy chain, cytoplasmic

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