SMTL ID : 7t92.1

Structure of the peroxisomal retro-translocon formed by a heterotrimeric ubiquitin ligase complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.10 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.367, I.369, C.370, C.387, C.390 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.367, A:C.370, A:C.387, A:C.390 ZN.7: 7 residues within 4Å: Chain B: C.306, C.308, Y.310, C.329, R.331, C.332, I.336 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.306, B:C.308, B:C.329, B:C.332 ZN.8: 6 residues within 4Å: Chain B: C.265, I.267, C.268, C.311, C.314 Chain C: Q.446 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.265, B:C.268, B:C.311, B:C.314 ZN.17: 6 residues within 4Å: Chain C: C.417, H.419, C.436, L.438, C.439, R.441 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.417, C:H.419, C:C.436, C:C.439 ZN.18: 4 residues within 4Å: Chain C: C.402, C.405, C.422, C.425 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.402, C:C.405, C:C.422, C:C.425

15 x LBN: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine(Non-covalent)

LBN.2: 18 residues within 4Å: Chain A: L.31, T.34, V.35, Y.37, L.38, V.68, H.71, Y.72, F.80, V.254, L.255, S.258, A.261, L.262, F.264, L.265, W.268, Y.269 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.31, A:T.34, A:L.38, A:F.80, A:A.261 pi-Cation interactions: A:Y.37 LBN.3: 9 residues within 4Å: Chain A: L.188, L.191, A.192, L.195, A.196, N.201 Chain B: V.68, L.72 Ligands: LBN.9 No protein-ligand interaction detected (PLIP) LBN.4: 9 residues within 4Å: Chain A: V.182, A.185, Y.186, S.189, F.193, P.207, F.208, C.210, L.211 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.182, A:L.211 LBN.5: 8 residues within 4Å: Chain A: L.132, K.135, L.136, A.139, V.167, A.168, W.171, R.172 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.171, A:W.171, A:W.171, A:W.171 Salt bridges: A:R.172 LBN.6: 11 residues within 4Å: Chain A: E.59, A.62, L.63, L.66, W.120, R.121, L.123, L.124, V.127, G.128, Y.131 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.62, A:L.66, A:W.120, A:L.124 LBN.9: 11 residues within 4Å: Chain A: L.188, L.191 Chain B: V.27, L.31, V.34, V.53, W.57, I.61, A.64, L.65 Ligands: LBN.3 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.64, B:L.65 LBN.12: 13 residues within 4Å: Chain A: F.260, F.264, W.267, W.268, F.273 Chain B: R.204, V.207, W.208, F.211, T.212, L.215 Chain C: G.276, Y.277 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.208, B:W.208, B:L.215 LBN.13: 9 residues within 4Å: Chain B: L.156, S.159, A.160, V.163, S.164, V.167, H.171, L.177, R.180 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.163 LBN.14: 7 residues within 4Å: Chain A: Y.37, V.41, Q.44 Chain B: L.231, A.232, W.235, R.236 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.236 LBN.15: 5 residues within 4Å: Chain B: A.67, F.70, K.71, W.75 Ligands: LBN.16 No protein-ligand interaction detected (PLIP) LBN.16: 9 residues within 4Å: Chain B: A.67, F.70, W.75, A.109, G.112, L.113, V.116, G.117 Ligands: LBN.15 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.70, B:W.75 LBN.20: 11 residues within 4Å: Chain C: F.218, A.221, T.222, V.225, T.229, A.231, Y.232, L.235, W.238, R.243 Ligands: LBN.22 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.235 Salt bridges: C:R.243 LBN.21: 12 residues within 4Å: Chain C: T.142, A.143, L.146, P.147, A.150, R.219, T.222, E.234, L.235, S.236, V.239 Ligands: LBN.22 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:T.142 Hydrogen bonds: C:A.143, C:L.235, C:S.236, C:S.236 Salt bridges: C:R.219 LBN.22: 14 residues within 4Å: Chain C: P.147, A.150, S.151, L.154, R.158, T.213, S.214, G.215, F.218, R.219, T.222, L.235 Ligands: LBN.20, LBN.21 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.154, C:F.218, C:F.218, C:L.235 Hydrogen bonds: C:S.151, C:G.215 Salt bridges: C:R.158 LBN.23: 10 residues within 4Å: Chain C: Y.204, H.208, P.211, L.212, H.217, M.288, R.291, A.292, H.295, V.296 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.212, C:L.212, C:H.217 Salt bridges: C:H.208, C:H.217, C:H.295, C:H.295

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.10: 7 residues within 4Å: Chain B: F.211, F.214, L.215, V.218, V.222, W.227 Ligands: CLR.19 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.215, B:V.222, B:W.227 CLR.11: 7 residues within 4Å: Chain B: V.114, G.118, R.119, W.122, L.153, S.154, H.157 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.122 CLR.19: 12 residues within 4Å: Chain B: F.214, F.217, V.218, L.221, V.222, R.226 Chain C: V.286, V.290, W.293, L.294, R.297 Ligands: CLR.10 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.221, B:L.221, C:V.290, C:V.290 Hydrogen bonds: B:R.226 CLR.24: 11 residues within 4Å: Chain B: L.162 Chain C: L.45, L.48, H.49, L.52, R.53, W.61, E.64, T.65, F.68 Ligands: CLR.25 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.48, C:W.61, C:W.61 CLR.25: 11 residues within 4Å: Chain C: W.61, E.64, T.67, F.68, A.71, I.144, V.145, H.148, L.149, R.152 Ligands: CLR.24 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.64, C:F.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, P. et al., A peroxisomal ubiquitin ligase complex forms a retrotranslocation channel. Nature (2022)

Release Date

2022-07-06

Peptides

Peroxin-12: A
Peroxin-2: B
Peroxin-10: C
Fab heavy chain: D
Fab light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
H

E
L

Membrane

We predict this structure to be a membrane protein.
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Peroxin-12

Peroxin-2

Peroxin-10

Fab heavy chain

Fab light chain