SMTL ID : 7kra.1

Cryo-EM structure of Saccharomyces cerevisiae ER membrane protein complex bound to Fab-DH4 in lipid nanodiscs

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-2-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: Q.171, V.191, N.192, Q.195 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.191 Hydrogen bonds: A:Q.195 NAG.2: 5 residues within 4Å: Chain A: P.86, T.88, E.91, N.106, S.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.106 NAG.3: 5 residues within 4Å: Chain A: D.52, N.54, R.55, N.73, S.75 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.73 NAG.5: 3 residues within 4Å: Chain G: L.113, N.115, T.117 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain G: N.53 No protein-ligand interaction detected (PLIP)

1 x X3P: [(2~{R})-1-octanoyloxy-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propan-2-yl] nonanoate(Non-covalent)

X3P.4: 7 residues within 4Å: Chain C: F.150, P.151, T.153 Chain D: P.166, W.175 Chain F: S.46, V.47 4 PLIP interactions: 2 interactions with chain F, 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: F:V.47, C:F.150, D:P.166 Hydrogen bonds: F:S.46

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
ER membrane protein complex subunit 5: E
ER membrane protein complex subunit 6: F
Protein SOP4: G
Endoplasmic reticulum membrane protein complex subunit 10: H
Fab DH4 heavy chain: I
Fab DH4 light chain: J
Unassigned helix: KL

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
J

K
M

L
N

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

ER membrane protein complex subunit 5

ER membrane protein complex subunit 6

Protein SOP4

Endoplasmic reticulum membrane protein complex subunit 10

Fab DH4 heavy chain

Fab DH4 light chain

Unassigned helix

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