SMTL ID : 7ado.1

Cryo-EM structure of human ER membrane protein complex in lipid nanodiscs

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.818, A.821 Chain D: M.174 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.818 NAG.2: 2 residues within 4Å: Chain A: N.370, S.394 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.370 NAG.3: 3 residues within 4Å: Chain A: Y.912, N.913 Chain G: F.149 No protein-ligand interaction detected (PLIP) NAG.9: 3 residues within 4Å: Chain I: S.141, H.142, N.183 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:H.142 Hydrogen bonds: I:N.183

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

PCW.4: 4 residues within 4Å: Chain A: W.498 Chain C: S.10, R.13 Chain E: F.22 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.13 PCW.5: 2 residues within 4Å: Chain A: Y.962, S.966 No protein-ligand interaction detected (PLIP) PCW.6: 5 residues within 4Å: Chain A: M.977, K.980 Chain C: M.29, Y.33, I.186 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.980, A:K.980 PCW.7: 8 residues within 4Å: Chain C: L.185, I.186 Chain E: K.7, I.60, I.63, A.64 Chain F: Y.28, F.99 6 PLIP interactions: 1 interactions with chain C, 2 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: C:L.185, F:F.99, E:K.7, E:I.60 pi-Cation interactions: F:Y.28 Salt bridges: E:K.7 PCW.8: 5 residues within 4Å: Chain F: R.73, S.80, R.81, R.82, F.85 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:R.81 Salt bridges: F:R.73, F:R.81, F:R.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller-Vedam, L.E. et al., Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients. Elife (2020)

Release Date

2020-12-02

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
Unassigned helix: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
K

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

Unassigned helix

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