SMTL ID : 8tqm.1

Cryo-EM structure of E3 ubiquitin ligase Doa10 from Saccharomyces cerevisiae

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

4 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.1: 29 residues within 4Å: Chain A: L.649, F.650, I.653, L.654, W.688, A.690, K.691, Y.692, G.694, M.695, K.698, P.712, E.713, L.790, T.793, K.794, L.797, E.798, V.803, K.804, L.807, M.980, V.983, T.984, I.1030, V.1033, C.1034, S.1037 Ligands: TGL.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.650, A:L.654, A:W.688, A:W.688, A:T.793, A:K.794, A:V.803 Salt bridges: A:K.691, A:K.691, A:K.698, A:K.804, A:K.804 PC1.2: 29 residues within 4Å: Chain A: F.689, Y.692, I.693, I.696, I.701, V.705, L.706, F.707, F.708, I.709, R.734, S.738, I.741, Y.742, F.745, F.815, F.827, I.828, V.906, Q.907, F.910, R.931, F.961, Y.965, L.968, L.969, V.972, W.973 Ligands: TGL.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.689, A:F.689, A:Y.692, A:I.693, A:L.706, A:F.708, A:F.708, A:F.708, A:I.709, A:I.741, A:Y.742, A:F.745, A:F.815, A:F.815, A:Y.965, A:L.969, A:V.972, A:W.973 PC1.4: 25 residues within 4Å: Chain A: W.149, N.150, G.153, K.154, T.157, Y.178, D.179, F.201, Q.205, I.209, L.212, H.213, Y.486, L.487, S.490, Y.491, H.568, I.570, R.573, A.574, A.577, L.578, Y.581 Ligands: PC1.5, ERG.7 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.212, A:L.487, A:Y.491, A:Y.491, A:A.574, A:A.577, A:L.578, A:Y.581 Hydrogen bonds: A:Y.178, A:Q.205 Salt bridges: A:D.179 PC1.5: 19 residues within 4Å: Chain A: Q.197, S.200, F.201, L.204, Q.205, M.208, I.209, I.211, L.212, A.215, I.570, F.627, W.670, P.672, F.673, L.675, F.676 Ligands: PC1.4, Y01.6 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.201, A:Q.205, A:I.209, A:I.211, A:A.215, A:I.570, A:W.670, A:L.675, A:F.676, A:F.676

1 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.3: 41 residues within 4Å: Chain A: L.645, L.649, F.650, I.653, I.681, L.684, Y.685, W.688, F.689, Y.692, G.749, F.750, H.753, L.767, L.787, L.790, Y.791, K.794, L.797, V.803, L.806, L.807, W.811, W.973, A.976, S.977, L.979, M.980, L.981, V.983, T.984, L.1028, I.1030, V.1033, S.1037, L.1040, S.1041, A.1044, I.1047 Ligands: PC1.1, PC1.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.645, A:L.684, A:Y.685, A:Y.685, A:W.688, A:W.688, A:F.750, A:L.767, A:L.787, A:L.790, A:Y.791, A:L.797, A:L.806, A:L.807, A:L.979, A:M.980, A:L.981, A:V.1033, A:L.1040

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.6: 8 residues within 4Å: Chain A: M.208, F.631, L.634, A.635, I.639, L.675, W.679 Ligands: PC1.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.631, A:I.639, A:W.679

1 x ERG: ERGOSTEROL(Non-covalent)

ERG.7: 13 residues within 4Å: Chain A: H.213, Y.486, I.489, S.490, P.494, I.497, L.501, T.580, Y.581, T.583, S.584, I.587 Ligands: PC1.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.486, A:I.497, A:I.497, A:L.501, A:Y.581

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, K. et al., Substrate recognition mechanism of the endoplasmic reticulum-associated ubiquitin ligase Doa10. Nat Commun (2024)

Release Date

2024-03-13

Peptides

ERAD-associated E3 ubiquitin-protein ligase DOA10: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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ERAD-associated E3 ubiquitin-protein ligase DOA10

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