SMTL ID : 7yg2.1

Cryo-EM structure of human IgM-Fc in complex with the J chain and the DBL domain of DBLMSP2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-10-1-mer

Ligands

1 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: 1 residues within 4Å: Chain L: N.48 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain B: N.370, S.372 Chain L: T.58 Ligands: NAG.3 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.370, B:S.372, B:S.372 NAG.3: 7 residues within 4Å: Chain B: L.368, N.370 Chain C: L.368, N.370, S.372 Ligands: NAG.2, NAG.4 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.368 Hydrogen bonds: C:S.372 NAG.4: 5 residues within 4Å: Chain C: L.368 Chain D: N.370, S.372 Ligands: NAG.3, NAG.5 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.368 Hydrogen bonds: D:S.372, D:S.372 NAG.5: 6 residues within 4Å: Chain D: N.370 Chain E: N.370 Chain F: N.370, S.372 Ligands: NAG.4, NAG.6 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D, 1 interactions with chain F Hydrogen bonds: E:N.370, D:N.370, F:S.372 NAG.6: 3 residues within 4Å: Chain F: N.370, S.372 Ligands: NAG.5 No protein-ligand interaction detected (PLIP) NAG.7: 4 residues within 4Å: Chain G: K.365, N.370, V.371 Ligands: NAG.8 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:K.361, G:N.370 NAG.8: 5 residues within 4Å: Chain G: N.370, S.372 Chain H: N.370 Ligands: NAG.7, NAG.9 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:N.370, G:S.372 NAG.9: 6 residues within 4Å: Chain I: N.370, S.372 Chain J: L.368, Y.369 Ligands: NAG.8, NAG.10 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.370 NAG.10: 4 residues within 4Å: Chain J: N.370, S.372 Chain K: L.368 Ligands: NAG.9 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:S.372 NAG.11: 6 residues within 4Å: Chain K: N.370 Chain L: R.4, R.20, E.34, N.36, I.37 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain K Hydrophobic interactions: L:N.36 Hydrogen bonds: L:R.20, L:R.20, K:N.370

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ji, C. et al., Plasmodium falciparum has evolved multiple mechanisms to hijack human immunoglobulin M. Nat Commun (2023)

Release Date

2023-03-29

Peptides

DBLMSP2: A
Immunoglobulin heavy constant mu: BCDEFGHIJK
Immunoglobulin J chain: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
A

C
B

D
C

E
D

F
E

G
F

H
G

I
H

J
K

K
L

L
J

DBLMSP2

Immunoglobulin heavy constant mu

Immunoglobulin J chain

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