SMTL ID : 7y0h.1

Cryo-EM structure of human IgM-Fc in complex with the J chain and the P. falciparum VAR2CSA FCR3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-10-1-1-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: 3 residues within 4Å: Chain I: N.48, S.50, D.51 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: N.370, S.372 Chain I: T.58 4 PLIP interactions: 1 interactions with chain I, 3 interactions with chain A Hydrogen bonds: I:T.58, A:N.370, A:S.372, A:S.372 NAG.3: 6 residues within 4Å: Chain A: L.368, N.370, V.371 Chain B: N.370, S.372 Ligands: NAG.4 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.368 Hydrogen bonds: B:N.370, B:S.372 NAG.4: 5 residues within 4Å: Chain B: L.368, N.370 Chain C: N.370, S.372 Ligands: NAG.3 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.372, C:S.372 Hydrophobic interactions: B:L.368 NAG.5: 3 residues within 4Å: Chain D: N.370, S.372 Ligands: NAG.6 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.370 NAG.6: 3 residues within 4Å: Chain D: T.367 Chain E: N.370 Ligands: NAG.5 No protein-ligand interaction detected (PLIP) NAG.7: 5 residues within 4Å: Chain F: K.365, N.370, V.371, S.372 Ligands: NAG.8 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.365, F:S.372 NAG.8: 5 residues within 4Å: Chain F: N.370, S.372 Chain G: N.370, S.372 Ligands: NAG.7 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.370, F:S.372 NAG.9: 7 residues within 4Å: Chain G: S.372 Chain H: N.370, S.372 Chain J: L.368, Y.369, N.370 Ligands: NAG.10 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:S.372 NAG.10: 4 residues within 4Å: Chain J: N.370 Chain K: L.368, N.370 Ligands: NAG.9 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:N.370 NAG.11: 5 residues within 4Å: Chain I: R.4, R.20, I.22, E.34 Chain K: N.370 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain K Hydrogen bonds: I:R.4, I:R.20, I: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

2023-04-12

Peptides

Immunoglobulin heavy constant mu: ABCDEFGHJK
Immunoglobulin J chain: I
Erythrocyte membrane protein 1: L

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
M

Immunoglobulin heavy constant mu

Immunoglobulin J chain

Erythrocyte membrane protein 1

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