SMTL ID : 7pfp.1

Full-length cryo-EM structure of the native human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 8 residues within 4Å: Chain A: H.75, N.76, C.77, A.79, S.101, G.103, L.104, G.105 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.79, A:G.103, A:G.103, A:L.104, A:G.105 NAG-NAG-FUC.9: 8 residues within 4Å: Chain C: H.75, N.76, C.77, A.79, S.101, G.103, L.104, G.105 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.79, C:G.103, C:G.103, C:L.104, C:G.105

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.2: 8 residues within 4Å: Chain A: S.78, A.79, N.80, F.98, G.105, C.106, T.107, D.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.108, A:D.108, A:D.108 NAG-NAG-BMA.10: 6 residues within 4Å: Chain C: S.78, A.79, N.80, C.106, T.107, D.108 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.108, C:D.108, C:D.108, C:D.108, C:D.108

2 x NAG- NAG- BMA- MAN- NAG- GAL- MAN- NAG- GAL: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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-NAG-GAL-MAN-NAG-GAL.3: 6 residues within 4Å: Chain A: W.230, N.232, G.233, K.246, C.248, C.256 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-GAL.11: 6 residues within 4Å: Chain C: W.230, N.232, G.233, K.246, C.248, C.256 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN.4: 13 residues within 4Å: Chain A: G.140, R.142, S.151, P.152, G.153, S.154, D.160, C.161, V.162, W.202, Q.263, N.275, T.277 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.152, A:S.151 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.12: 13 residues within 4Å: Chain C: G.140, R.142, S.151, P.152, G.153, S.154, D.160, C.161, V.162, W.202, Q.263, N.275, T.277 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.152, C:S.151

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

NAG-NAG-BMA-FUC.5: 5 residues within 4Å: Chain A: Q.316, C.317, Q.319, F.321, N.322 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.319, A:Q.319 NAG-NAG-BMA-FUC.13: 5 residues within 4Å: Chain C: Q.316, C.317, Q.319, F.321, N.322 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.319, C:Q.319

2 x NAG- NAG- BMA- MAN- NAG- GAL- NAG- MAN- NAG: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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-NAG-GAL-NAG-MAN-NAG.6: 9 residues within 4Å: Chain A: N.396, H.399, T.401, S.426 Chain B: N.447, I.448, R.449, G.451, T.453 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.449, B:G.451, B:T.453 NAG-NAG-BMA-MAN-NAG-GAL-NAG-MAN-NAG.14: 9 residues within 4Å: Chain A: N.447, I.448, R.449, G.451, T.453 Chain C: N.396, H.399, T.401, S.426 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.449, A:G.451

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

NAG-NAG-BMA-MAN-MAN-FUC.7: 4 residues within 4Å: Chain A: N.513, T.515, D.516, P.517 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-FUC.8: 4 residues within 4Å: Chain B: N.513, T.515, D.516, P.517 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stsiapanava, A. et al., Structure of the decoy module of human glycoprotein 2 and uromodulin and its interaction with bacterial adhesin FimH. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-03-16

Peptides

Uromodulin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Uromodulin

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