SMTL ID : 9di3.1

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: 22 residues within 4Å: Chain A: F.830, S.831, M.832, F.836, K.858, A.859, G.860, C.861, 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, H.1336 20 PLIP interactions: 20 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:T.864, A:A.865, A:D.938, A:S.1007, A:K.1008, A:H.1011 Salt bridges: A:K.863, A:K.863, A:K.863, A:R.1332, A:R.1332, A:R.1335, A:R.1335, A:R.1335

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

ADP.2: 13 residues within 4Å: Chain A: L.552, I.553, A.581, G.582, G.584, K.585, T.586, E.587, D.631, E.632, I.712, R.754, K.757 15 PLIP interactions: 15 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:D.631, A:E.632, A:E.632, A:R.754, A:R.754 Salt bridges: A:K.585, A:K.585 ADP.3: 10 residues within 4Å: Chain A: M.1515, A.1544, R.1546, T.1547, G.1548, K.1549, T.1550, I.1551, W.1703, I.1776 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.1546, A:R.1546, A:T.1547, A:T.1547, A:G.1548, A:K.1549, A:T.1550, A:T.1550, A:I.1551 Salt bridges: A:K.1549 ADP.4: 16 residues within 4Å: Chain A: I.1175, T.1180, G.1204, S.1205, G.1206, K.1207, T.1208, M.1209, I.1353, Y.1357, R.1403, T.1406, R.1410, P.1689, A.1690, R.1694 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:T.1180, A:T.1180, A:G.1204, A:G.1206, A:K.1207, A:T.1208, A:T.1208, A:T.1208, A:M.1209, A:R.1410, A:R.1694, A:R.1694 Salt bridges: A:K.1207, A:K.1207, A:R.1403, A:R.1403

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

Related Entries With Identical Sequence