SMTL ID : 7y0j.1

Cryo-EM structure of human IgM-Fc in complex with the J chain and the P. falciparum TM284VAR1

Coordinates

PDB Format Compare

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: L.368, N.370, S.372 Ligands: NAG.3 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.368 Hydrogen bonds: B:S.372 NAG.3: 6 residues within 4Å: Chain B: L.368, N.370 Chain C: N.370, S.372 Ligands: NAG.2, NAG.4 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.372 Hydrophobic interactions: B:L.368 NAG.4: 4 residues within 4Å: Chain C: L.368 Chain D: N.370 Ligands: NAG.3, NAG.5 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.368 NAG.5: 3 residues within 4Å: Chain E: N.370 Ligands: NAG.4, NAG.6 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.370 NAG.6: 4 residues within 4Å: Chain E: T.367 Chain F: N.370, S.372 Ligands: NAG.5 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:T.367 Hydrogen bonds: F:N.370, F:S.372 NAG.7: 2 residues within 4Å: Chain G: N.370 Ligands: NAG.8 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:K.365 NAG.8: 5 residues within 4Å: Chain G: S.372 Chain H: N.370, S.372 Ligands: NAG.7, NAG.9 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:S.372 NAG.9: 4 residues within 4Å: Chain I: N.370, S.372 Ligands: NAG.8, NAG.10 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.370 NAG.10: 4 residues within 4Å: Chain I: S.372 Chain J: N.370 Ligands: NAG.9, NAG.11 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:N.370 NAG.11: 4 residues within 4Å: Chain J: N.370 Chain K: L.368, N.370 Ligands: NAG.10 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain J Hydrogen bonds: K:N.370, J: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

2023-04-05

Peptides

Erythrocyte membrane protein 2 variant TM284var1: 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

Erythrocyte membrane protein 2 variant TM284var1

Immunoglobulin heavy constant mu

Immunoglobulin J chain

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