SMTL ID : 9eq3.1

Structure of IgE HMM5 bound to FceRIa cryo-EM class 8

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-mer

Ligands

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 8 residues within 4Å: Chain A: R.331, Y.336, S.338, L.356, V.358, D.359, Q.389, N.391 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.338, A:Y.336 NAG-NAG-BMA-MAN-MAN.5: 5 residues within 4Å: Chain C: G.16, E.17, N.18, V.53, N.54 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.53 NAG-NAG-BMA-MAN-MAN.9: 7 residues within 4Å: Chain C: K.114, I.116 Chain D: Y.336, D.359, Q.389, N.391, T.393 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.336, D:Y.336

1 x NAG- NAG- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN-MAN.2: 9 residues within 4Å: Chain A: R.416, R.424 Chain C: H.38, N.39, F.57, E.58, S.60, G.61, Y.77 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.416, C:S.60

4 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 2 residues within 4Å: Chain C: V.70, N.71 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 2 residues within 4Å: Chain C: E.45, N.47 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 2 residues within 4Å: Chain C: T.145, N.163 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 3 residues within 4Å: Chain C: W.10, R.103, N.132 No protein-ligand interaction detected (PLIP)

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.8: 4 residues within 4Å: Chain C: E.96, G.97, T.136, N.137 No protein-ligand interaction detected (PLIP)

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

NAG.10: 1 residues within 4Å: Chain A: N.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.165 NAG.11: 3 residues within 4Å: Chain A: R.202, V.213, N.215 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain A: N.137, T.139 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.137 NAG.13: 6 residues within 4Å: Chain A: T.260, I.261, N.262, T.312, Q.314, G.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.314, A:G.315 NAG.14: 1 residues within 4Å: Chain D: N.137 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.136 NAG.15: 3 residues within 4Å: Chain D: D.160, R.202, N.215 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.160, D:N.215 NAG.16: 3 residues within 4Å: Chain D: N.262, T.264, V.274 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.262 NAG.17: 3 residues within 4Å: Chain D: T.161, L.164, N.165 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jensen, R.K. et al., The dynamics of hinge flexibility in receptor bound immunoglobulin E revealed by electron microscopy. Biorxiv (2023)

Release Date

2024-04-10

Peptides

IgE HMM5 heavy chain: AD
IgE HMM5 light chain: BE
High affinity immunoglobulin epsilon receptor subunit alpha: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

D
X

B
L

E
Y

C
R

IgE HMM5 heavy chain

IgE HMM5 light chain

High affinity immunoglobulin epsilon receptor subunit alpha

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