SMTL ID : 8s9s.1

Structure of the human ER membrane protein complex (EMC) in GDN

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: V.27, N.913 Chain G: F.149 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.27 NAG-NAG.2: 5 residues within 4Å: Chain A: N.818, A.821, D.826 Chain I: C.168, R.169 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain I: S.143, N.182, S.184 No protein-ligand interaction detected (PLIP)

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

NAG.4: 3 residues within 4Å: Chain A: F.369, N.370, S.394 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.369 Hydrogen bonds: A:N.370, A:S.394

6 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PCW.5: 8 residues within 4Å: Chain A: F.970, V.973, T.976, M.977 Chain C: F.25, F.26, Y.33, I.186 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.970, A:V.973, A:V.973, C:F.26 Salt bridges: A:K.980 PCW.6: 8 residues within 4Å: Chain C: I.30, R.31, V.34, T.116, P.120, L.123, I.124, W.127 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.123, C:I.124 Hydrogen bonds: C:T.116 PCW.7: 14 residues within 4Å: Chain C: F.25, I.182, S.184, L.185, I.186, G.188, Q.189 Chain E: K.7, L.17, I.63 Chain F: Y.28, L.36, A.39, F.99 9 PLIP interactions: 5 interactions with chain C, 1 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: C:F.25, C:I.182, C:L.185, C:I.186, C:I.186, E:L.17, F:L.36, F:A.39, F:F.99 PCW.8: 9 residues within 4Å: Chain A: W.498 Chain C: N.11, R.13, L.14, L.18 Chain E: A.21, F.22, A.25 Chain F: M.106 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:A.21, E:F.22, E:F.22, E:A.25, C:L.18 Salt bridges: C:R.13 PCW.9: 5 residues within 4Å: Chain C: P.143 Chain D: F.167 Chain F: G.48, L.49, F.52 No protein-ligand interaction detected (PLIP) PCW.10: 5 residues within 4Å: Chain F: I.67, R.72, R.73, W.74, R.81 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:R.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pleiner, T. et al., A selectivity filter in the ER membrane protein complex limits protein misinsertion at the ER. J.Cell Biol. (2023)

Release Date

2023-05-17

Peptides

ER membrane protein complex subunit 1: A
ER membrane protein complex subunit 2: B
ER membrane protein complex subunit 3: C
ER membrane protein complex subunit 4: D
Membrane magnesium transporter 1: E
ER membrane protein complex subunit 6: F
ER membrane protein complex subunit 7: G
ER membrane protein complex subunit 8: H
ER membrane protein complex subunit 10: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
5

F
6

G
7

H
8

I
10

Membrane

We predict this structure to be a membrane protein.
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ER membrane protein complex subunit 1

ER membrane protein complex subunit 2

ER membrane protein complex subunit 3

ER membrane protein complex subunit 4

Membrane magnesium transporter 1

ER membrane protein complex subunit 6

ER membrane protein complex subunit 7

ER membrane protein complex subunit 8

ER membrane protein complex subunit 10

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