SMTL ID : 7qsr.1

CryoEM structure of the Ectodomain of Human PLA2R

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

2 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.1: 9 residues within 4Å: Chain A: N.73, S.75, A.76, Q.79, Y.84, L.90, V.91, K.1120, M.1124 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 7 residues within 4Å: Chain A: N.699, H.703, W.708, T.709, E.710, A.759, N.760 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.708

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.3: 8 residues within 4Å: Chain A: F.74, P.77, L.106, Y.108, R.122, N.1112, F.1206, Q.1208 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.122

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

NAG-NAG-BMA-MAN.4: 6 residues within 4Å: Chain A: N.963, T.965, H.966, C.1067, G.1068, E.1070 No protein-ligand interaction detected (PLIP)

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

NAG.5: 3 residues within 4Å: Chain A: N.434, D.435, S.436 No protein-ligand interaction detected (PLIP) NAG.6: 4 residues within 4Å: Chain A: F.451, P.452, N.453, R.454 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain A: Q.563, N.564 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain A: F.706, N.707 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.707 NAG.9: 3 residues within 4Å: Chain A: A.862, N.889, Q.890 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.889 NAG.10: 1 residues within 4Å: Chain A: N.1103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1103 NAG.11: 2 residues within 4Å: Chain A: E.412, N.413 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.413, A:N.413 NAG.12: 3 residues within 4Å: Chain A: E.884, N.1036, E.1039 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1036 NAG.13: 4 residues within 4Å: Chain A: D.1300, G.1301, N.1302, N.1303 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.1302 Hydrogen bonds: A:G.1301, A:N.1302, A:N.1303

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fresquet, M. et al., Structure of PLA2R reveals presentation of the dominant membranous nephropathy epitope and an immunogenic patch. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-07-20

Peptides

Secretory phospholipase A2 receptor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Secretory phospholipase A2 receptor