SMTL ID : 7ytd.1

Cryo-EM structure of four human FcmR bound to IgM-Fc/J

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-10-1-4-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: N.219 Ligands: NAG.2 No protein-ligand interaction detected (PLIP) NAG.2: 4 residues within 4Å: Chain A: N.219 Chain B: N.219 Ligands: NAG.1, NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.219 NAG.3: 5 residues within 4Å: Chain B: N.219 Chain C: N.219, S.221 Ligands: NAG.2, NAG.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.219 NAG.4: 6 residues within 4Å: Chain C: N.219 Chain D: N.219, S.221 Chain E: S.221 Ligands: NAG.3, NAG.5 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.219, D:N.219 NAG.5: 3 residues within 4Å: Chain E: N.219, S.221 Ligands: NAG.4 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.221 NAG.6: 2 residues within 4Å: Chain F: N.219 Ligands: NAG.7 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.219 NAG.7: 3 residues within 4Å: Chain G: N.219 Ligands: NAG.6, NAG.8 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:S.221, G:N.219 NAG.8: 5 residues within 4Å: Chain H: N.219, S.221 Chain J: N.219 Ligands: NAG.7, NAG.9 No protein-ligand interaction detected (PLIP) NAG.9: 6 residues within 4Å: Chain J: N.219, V.220, S.221 Chain K: N.219 Ligands: NAG.8, NAG.10 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:N.219 NAG.10: 5 residues within 4Å: Chain I: R.20, I.22 Chain K: N.219, S.221 Ligands: NAG.9 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:R.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Immunoglobulin M perception by Fc mu R. Nature (2023)

Release Date

2023-02-01

Peptides

Immunoglobulin heavy constant mu: ABCDEFGHJK
Immunoglobulin J chain: I
Fas apoptotic inhibitory molecule 3: LMNO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

J
K

K
L

I
J

L
R

M
S

N
U

O
V

Immunoglobulin heavy constant mu

Immunoglobulin J chain

Fas apoptotic inhibitory molecule 3

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