SMTL ID : 9dkj.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: 20 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, V.1002, C.1003, S.1007, K.1008, H.1011, E.1068, R.1290, R.1332, R.1335 17 PLIP interactions: 17 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:A.865, A:E.978, A:E.1068 Salt bridges: A:K.863, A:K.863, A:R.1290, A:R.1332, A:R.1335, A:R.1335, A:R.1335

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

ADP.2: 14 residues within 4Å: Chain A: M.1515, V.1516, H.1518, R.1546, T.1547, G.1548, K.1549, T.1550, I.1551, W.1703, I.1776, R.1780, E.2252, R.2295 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:V.1516, A:V.1516, A:R.1546, A:R.1546, A:T.1547, A:G.1548, 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 pi-Cation interactions: A:R.1546 ADP.3: 17 residues within 4Å: Chain A: L.552, I.553, T.555, A.581, G.582, T.583, G.584, K.585, T.586, E.587, I.712, L.753, R.754, K.757, R.761, D.955 Ligands: MG.5 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:E.587, A:K.757, A:R.761, A:D.955, A:D.955 Salt bridges: A:K.585, A:R.754, A:R.754, A:R.992 ADP.4: 20 residues within 4Å: Chain A: V.1174, I.1175, T.1177, T.1180, P.1202, P.1203, G.1204, S.1205, G.1206, K.1207, T.1208, M.1209, P.1345, I.1353, Y.1354, Y.1357, P.1402, R.1403, T.1406 Ligands: MG.6 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:I.1175, A:T.1177, A:T.1180, A:G.1204, A:S.1205, A:G.1206, A:K.1207, A:T.1208, A:T.1208, A:T.1208, A:M.1209 Salt bridges: A:K.1207, A:R.1403, A:R.1403

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: T.586, D.631, T.680 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.586 MG.6: 3 residues within 4Å: Chain A: R.1403, N.1693 Ligands: ADP.4 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

2025-05-28

Peptides

Dynein heavy chain, cytoplasmic: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dynein heavy chain, cytoplasmic

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