SMTL ID : 7d3e.1

Cryo-EM structure of human DUOX1-DUOXA1 in low-calcium state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN-MAN-MAN.1: 33 residues within 4Å: Chain B: K.15, F.18, M.20, D.21, T.22, S.74, Y.87, N.109, E.122, T.123, I.124, N.125, Y.126, N.127, E.128, E.129, K.148 Chain C: D.61, V.63, Y.64, P.119, E.121, W.151, G.156, R.157, P.159, Y.1064, F.1068, A.1069, A.1070, H.1071, H.1072, D.1077 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:F.18, C:Y.1064 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2: 33 residues within 4Å: Chain A: D.61, V.63, Y.64, P.119, E.121, W.151, G.156, R.157, P.159, Y.1064, F.1068, A.1069, A.1070, H.1071, H.1072, D.1077 Chain D: K.15, F.18, M.20, D.21, T.22, S.74, Y.87, N.109, E.122, T.123, I.124, N.125, Y.126, N.127, E.128, E.129, K.148 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Y.1064, D:F.18

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.3: 21 residues within 4Å: Chain A: F.1097, I.1100, L.1101, M.1104, R.1106, H.1130, R.1131, A.1134, M.1205, Y.1206, A.1209, F.1221, W.1222, H.1225, H.1226, Y.1228, L.1231, Y.1232, Y.1260, K.1264 Ligands: FAD.6 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:F.1097, A:I.1100, A:L.1101, A:M.1104, A:R.1131, A:Y.1206, A:Y.1206, A:F.1221, A:W.1222, A:Y.1228, A:Y.1228, A:L.1231, A:Y.1260 Salt bridges: A:R.1106, A:R.1106, A:K.1264 pi-Stacking: A:F.1221, A:Y.1228 Metal complexes: A:H.1130, A:H.1225 HEM.4: 25 residues within 4Å: Chain A: R.1087, A.1090, I.1093, S.1094, F.1097, T.1141, H.1144, S.1145, H.1148, P.1191, G.1195, L.1198, L.1199, L.1202, L.1235, H.1238, G.1239, F.1241, A.1242, L.1243, I.1244, Q.1245, P.1247, R.1248, F.1249 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:A.1090, A:F.1097, A:T.1141, A:H.1148, A:P.1191, A:L.1198, A:L.1199, A:L.1199, A:L.1243, A:F.1249 Hydrogen bonds: A:G.1239, A:A.1242, A:L.1243, A:I.1244, A:Q.1245, A:R.1248, A:F.1249 pi-Cation interactions: A:H.1148 Metal complexes: A:H.1144, A:H.1238 HEM.14: 21 residues within 4Å: Chain C: F.1097, I.1100, L.1101, M.1104, R.1106, H.1130, R.1131, A.1134, M.1205, Y.1206, A.1209, F.1221, W.1222, H.1225, H.1226, Y.1228, L.1231, Y.1232, Y.1260, K.1264 Ligands: FAD.17 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:F.1097, C:I.1100, C:L.1101, C:M.1104, C:R.1131, C:Y.1206, C:Y.1206, C:F.1221, C:W.1222, C:Y.1228, C:Y.1228, C:L.1231, C:Y.1260 Salt bridges: C:R.1106, C:R.1106, C:K.1264 pi-Stacking: C:H.1130, C:F.1221, C:Y.1228 Metal complexes: C:H.1225 HEM.15: 25 residues within 4Å: Chain C: R.1087, A.1090, I.1093, S.1094, F.1097, T.1141, H.1144, S.1145, H.1148, P.1191, G.1195, L.1198, L.1199, L.1202, L.1235, H.1238, G.1239, F.1241, A.1242, L.1243, I.1244, Q.1245, P.1247, R.1248, F.1249 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:A.1090, C:F.1097, C:T.1141, C:H.1148, C:P.1191, C:L.1198, C:L.1199, C:L.1199, C:L.1243, C:F.1249 Hydrogen bonds: C:G.1239, C:A.1242, C:L.1243, C:I.1244, C:Q.1245, C:R.1248, C:F.1249 Metal complexes: C:H.1144

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.5: 21 residues within 4Å: Chain A: R.1036, E.1039, N.1040, Y.1041, G.1388, G.1389, I.1390, G.1391, V.1422, T.1423, R.1424, T.1455, R.1495, C.1520, G.1521, P.1522, G.1524, M.1525, N.1528, E.1549, N.1550 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.1390 Hydrogen bonds: A:R.1036, A:E.1039, A:N.1040, A:Y.1041, A:Y.1041, A:I.1390, A:T.1423, A:T.1455, A:T.1455, A:R.1495, A:G.1521, A:N.1528, A:E.1549 Salt bridges: A:R.1036, A:R.1424, A:R.1424, A:R.1495 pi-Cation interactions: A:R.1036, A:R.1036 NDP.16: 21 residues within 4Å: Chain C: R.1036, E.1039, N.1040, Y.1041, G.1388, G.1389, I.1390, G.1391, V.1422, T.1423, R.1424, T.1455, R.1495, C.1520, G.1521, P.1522, G.1524, M.1525, N.1528, E.1549, N.1550 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:I.1390 Hydrogen bonds: C:R.1036, C:E.1039, C:N.1040, C:Y.1041, C:Y.1041, C:I.1390, C:T.1423, C:T.1455, C:T.1455, C:R.1495, C:G.1521, C:N.1528, C:E.1549 Salt bridges: C:R.1036, C:R.1424, C:R.1424, C:R.1495 pi-Cation interactions: C:R.1036, C:R.1036

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.6: 22 residues within 4Å: Chain A: R.1113, D.1124, V.1127, D.1128, R.1131, R.1214, W.1305, Y.1318, H.1319, P.1320, F.1321, T.1322, H.1335, I.1336, R.1337, A.1339, G.1340, P.1341, W.1342, T.1343, T.1393 Ligands: HEM.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:W.1305, A:P.1320 Hydrogen bonds: A:D.1128, A:D.1128, A:Y.1318, A:P.1320, A:T.1322, A:T.1322, A:H.1335, A:R.1337, A:G.1340, A:W.1342, A:T.1343 Salt bridges: A:R.1131, A:R.1214, A:R.1214, A:H.1319 pi-Stacking: A:F.1321 FAD.17: 22 residues within 4Å: Chain C: R.1113, D.1124, V.1127, D.1128, R.1131, R.1214, W.1305, Y.1318, H.1319, P.1320, F.1321, T.1322, H.1335, I.1336, R.1337, A.1339, G.1340, P.1341, W.1342, T.1343, T.1393 Ligands: HEM.14 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:W.1305, C:P.1320 Hydrogen bonds: C:D.1128, C:D.1128, C:Y.1318, C:P.1320, C:T.1322, C:T.1322, C:H.1335, C:R.1337, C:G.1340, C:W.1342, C:T.1343 Salt bridges: C:R.1131, C:R.1214, C:R.1214, C:H.1319 pi-Stacking: C:F.1321

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

NAG.7: 6 residues within 4Å: Chain A: N.94, I.392, W.559, H.560, K.561, Q.567 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.94, A:H.560, A:K.561, A:Q.567 NAG.8: 4 residues within 4Å: Chain A: K.527, E.530, E.531, N.534 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.530, A:E.531 Hydrogen bonds: A:N.534 NAG.9: 4 residues within 4Å: Chain A: N.342, A.343, S.344, H.346 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain B: S.82, T.83, N.84 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.84 NAG.13: 2 residues within 4Å: Chain B: N.121 Chain C: H.71 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.71 NAG.18: 6 residues within 4Å: Chain C: N.94, I.392, W.559, H.560, K.561, Q.567 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.94, C:H.560, C:K.561, C:Q.567 NAG.19: 4 residues within 4Å: Chain C: K.527, E.530, E.531, N.534 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:E.530, C:E.531 Hydrogen bonds: C:N.534 NAG.20: 4 residues within 4Å: Chain C: N.342, A.343, S.344, H.346 No protein-ligand interaction detected (PLIP) NAG.23: 3 residues within 4Å: Chain D: S.82, T.83, N.84 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.84 NAG.24: 2 residues within 4Å: Chain A: H.71 Chain D: N.121 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.71

4 x NA: SODIUM ION(Non-functional Binders)

NA.10: 4 residues within 4Å: Chain A: T.332, R.395, D.397, V.399 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.332 NA.11: 5 residues within 4Å: Chain A: D.109, T.170, W.172, D.174, S.176 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.170, A:T.170, A:D.174, A:S.176 NA.21: 4 residues within 4Å: Chain C: T.332, R.395, D.397, V.399 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.332 NA.22: 5 residues within 4Å: Chain C: D.109, T.170, W.172, D.174, S.176 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.170, C:D.174, C:S.176, C:S.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, J.X. et al., Structures of human dual oxidase 1 complex in low-calcium and high-calcium states. Nat Commun (2021)

Release Date

2020-12-09

Peptides

Dual oxidase 1: AC
Isoform 2 of Dual oxidase maturation factor 1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Membrane

We predict this structure to be a membrane protein.
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Dual oxidase 1

Isoform 2 of Dual oxidase maturation factor 1

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