SMTL ID : 6wb9.1

Structure of the S. cerevisiae ER membrane complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 6 residues within 4Å: Chain B: N.54, R.55, N.73, S.75, S.76, L.80 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.54, B:R.55, B:S.75 NAG.2: 6 residues within 4Å: Chain B: T.65, P.86, T.88, E.91, N.106, S.109 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.88 Hydrogen bonds: B:N.106 NAG.3: 5 residues within 4Å: Chain B: F.173, V.191, N.192, Q.195, M.197 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.191 Hydrogen bonds: B:F.173, B:Q.195 NAG.6: 5 residues within 4Å: Chain H: G.52, N.53, T.87, Y.89, F.132 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:F.132 NAG.7: 2 residues within 4Å: Chain H: V.84, N.85 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain H: N.115, T.117 No protein-ligand interaction detected (PLIP)

2 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.4: 13 residues within 4Å: Chain D: F.150, P.151, L.152, T.153, F.156 Chain E: L.107, L.164, W.172, W.175 Chain G: S.46, V.47, I.93, V.97 15 PLIP interactions: 5 interactions with chain D, 3 interactions with chain G, 7 interactions with chain E Hydrophobic interactions: D:F.150, D:F.150, D:T.153, D:F.156, D:F.156, G:I.93, G:V.97, E:L.107, E:L.107, E:L.164, E:W.172, E:W.175 Hydrogen bonds: G:S.46, E:W.175, E:W.175 POV.5: 15 residues within 4Å: Chain D: S.16, V.190, L.193 Chain F: Y.9, A.13, L.16, F.17, F.60, S.67 Chain G: F.26, L.33, V.34, L.37, F.41, F.102 14 PLIP interactions: 6 interactions with chain G, 6 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: G:L.33, G:V.34, G:L.37, G:L.37, G:F.41, G:F.102, F:Y.9, F:A.13, F:L.16, F:F.17, F:F.60, D:V.190, D:L.193 Hydrogen bonds: F:S.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bai, L. et al., Structure of the ER membrane complex, a transmembrane-domain insertase. Nature (2020)

Release Date

2020-06-03

Peptides

Endoplasmic reticulum membrane protein complex subunit 10: A
ER membrane protein complex subunit 1: B
ER membrane protein complex subunit 2: C
ER membrane protein complex subunit 3: D
ER membrane protein complex subunit 4: E
ER membrane protein complex subunit 5: F
ER membrane protein complex subunit 6: G
Protein SOP4: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
0

B
1

C
2

D
3

E
4

F
5

G
6

H
7

Membrane

We predict this structure to be a membrane protein.
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Endoplasmic reticulum membrane protein complex subunit 10

ER membrane protein complex subunit 1

ER membrane protein complex subunit 2

ER membrane protein complex subunit 3

ER membrane protein complex subunit 4

ER membrane protein complex subunit 5

ER membrane protein complex subunit 6

Protein SOP4

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