SMTL ID : 8dzz.1

Cryo-EM structure of chi dynein bound to Lis1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-4-mer

Ligands

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

ATP.1: 18 residues within 4Å: Chain A: F.830, S.831, 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, E.1294, R.1332, R.1335 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:T.864, A:A.865, A:K.1008, A:E.1068, A:E.1068, A:E.1294 Salt bridges: A:K.863, A:K.863, A:R.1332, A:R.1335, A:R.1335 pi-Stacking: A:F.830, A:F.830 ATP.2: 19 residues within 4Å: Chain A: L.552, I.553, A.581, G.582, T.583, G.584, K.585, T.586, E.587, E.632, N.682, I.712, L.753, R.754, K.757, R.761, D.955, A.988, R.992 20 PLIP interactions: 20 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:N.682, A:K.757, A:R.761 Salt bridges: A:K.585, A:K.585, A:R.754, A:R.754, A:R.754, A:R.992 ATP.4: 15 residues within 4Å: Chain A: I.1175, P.1203, G.1204, G.1206, K.1207, T.1208, M.1209, N.1319, I.1353, Y.1354, Y.1357, P.1402, R.1403, T.1406, N.1693 14 PLIP interactions: 14 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:M.1209, A:D.1270, A:N.1319, A:R.1403, A:N.1693 Salt bridges: A:K.1207, A:K.1207, A:R.1403 ATP.5: 18 residues within 4Å: Chain D: F.830, S.831, 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, E.1294, R.1332, R.1335 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:S.831, D:S.831, D:G.860, D:G.862, D:K.863, D:T.864, D:T.864, D:T.864, D:A.865, D:K.1008, D:E.1068, D:E.1068, D:E.1294 Salt bridges: D:K.863, D:K.863, D:R.1332, D:R.1335, D:R.1335 pi-Stacking: D:F.830, D:F.830 ATP.6: 19 residues within 4Å: Chain D: L.552, I.553, A.581, G.582, T.583, G.584, K.585, T.586, E.587, E.632, N.682, I.712, L.753, R.754, K.757, R.761, D.955, A.988, R.992 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:I.553, D:I.553, D:G.582, D:T.583, D:G.584, D:K.585, D:T.586, D:T.586, D:E.587, D:E.632, D:E.632, D:N.682, D:K.757, D:R.761 Salt bridges: D:K.585, D:K.585, D:R.754, D:R.754, D:R.754, D:R.992 ATP.8: 13 residues within 4Å: Chain D: P.1203, G.1204, G.1206, K.1207, T.1208, M.1209, D.1270, Q.1271, N.1319, I.1353, R.1403, T.1406, N.1693 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:G.1204, D:G.1206, D:K.1207, D:T.1208, D:T.1208, D:M.1209, D:Q.1271, D:N.1319, D:N.1693 Salt bridges: D:K.1207, D:K.1207, D:R.1403, D:R.1403, D:R.1403

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

ADP.3: 14 residues within 4Å: Chain A: M.1515, V.1516, H.1518, S.1545, R.1546, T.1547, G.1548, K.1549, T.1550, I.1551, W.1703, I.1776, R.1780, R.2295 15 PLIP interactions: 15 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: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.7: 14 residues within 4Å: Chain D: M.1515, V.1516, H.1518, S.1545, R.1546, T.1547, G.1548, K.1549, T.1550, I.1551, W.1703, I.1776, R.1780, R.2295 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:V.1516, D:V.1516, D:R.1546, D:R.1546, D:T.1547, D:G.1548, D:K.1549, D:T.1550, D:T.1550, D:I.1551, D:R.1780, D:R.1780 Salt bridges: D:K.1549, D:R.2295, D:R.2295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karasmanis, E.P. et al., Lis1 relieves cytoplasmic dynein-1 autoinhibition by acting as a molecular wedge. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-08-30

Peptides

Dynein heavy chain, cytoplasmic: AD
Nuclear distribution protein PAC1: BCEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

C
C

E
E

F
F

Dynein heavy chain, cytoplasmic

Nuclear distribution protein PAC1

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