SMTL ID : 9inh.1

Cryo-EM structure of human XPR1 in complex with InsP6 in outward-facing state (SPX visible)-in the presence of KIDINS220-1-432 and 10 mM KH2PO4

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 10 residues within 4Å: Chain A: M.1, K.2, F.3, K.158, K.162, K.165, R.308, K.364, Y.368, K.369 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:M.1, A:M.1, A:K.2, A:K.165 Salt bridges: A:K.2, A:K.2, A:K.2, A:K.158, A:K.158, A:K.158, A:K.162, A:K.165, A:R.308, A:K.364, A:K.369, A:K.369 IHP.18: 10 residues within 4Å: Chain B: M.1, K.2, F.3, K.158, K.162, K.165, R.308, K.364, Y.368, K.369 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:M.1, B:K.2 Salt bridges: B:K.2, B:K.2, B:K.158, B:K.158, B:K.158, B:K.162, B:K.165, B:R.308, B:K.364

12 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 6 residues within 4Å: Chain A: Y.558, C.561, E.565, F.602, F.605, F.609 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.558, A:Y.558, A:E.565, A:F.602, A:F.605, A:F.609 CLR.4: 7 residues within 4Å: Chain A: G.446, A.449, I.450, W.457, F.487, T.491, A.494 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.449, A:I.450, A:W.457, A:A.494 CLR.5: 5 residues within 4Å: Chain A: L.407, E.411, I.414, V.451, I.454 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.407, A:E.411, A:I.414, A:V.451 CLR.6: 5 residues within 4Å: Chain A: P.338, I.339 Chain B: L.253, F.257 Ligands: 3PE.19 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.253, B:F.257 CLR.7: 4 residues within 4Å: Chain A: F.511, T.574, I.577, S.581 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.511, A:T.574, A:I.577 CLR.10: 5 residues within 4Å: Chain A: L.410, M.413, Y.417, S.418, W.423 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.423 CLR.25: 6 residues within 4Å: Chain B: Y.553, C.561, E.565, F.602, F.605, F.609 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.553, B:E.565, B:F.602, B:F.605, B:F.609 CLR.27: 8 residues within 4Å: Chain B: G.446, A.449, I.450, C.453, F.487, T.491, A.494, L.495 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.449, B:I.450, B:A.494 CLR.28: 4 residues within 4Å: Chain B: L.407, E.411, I.414, I.454 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.407, B:E.411, B:I.414 CLR.29: 3 residues within 4Å: Chain A: L.253 Chain B: I.339 Ligands: 3PE.17 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.253 CLR.30: 7 residues within 4Å: Chain B: F.511, I.515, Y.518, T.574, I.577, S.578, S.581 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.511, B:F.511, B:I.515, B:Y.518, B:T.574, B:I.577 Hydrogen bonds: B:S.581 CLR.33: 7 residues within 4Å: Chain B: V.356, L.410, M.413, I.414, Y.417, S.418, W.423 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.356, B:L.410, B:I.414, B:W.423

6 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.3: 21 residues within 4Å: Chain A: L.278, F.281, L.285, W.292, L.305, N.306, S.309, N.310, L.311, L.316, I.319, L.323, F.358, K.369, S.370, W.373, L.374, W.395, L.400, L.403, I.406 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.278, A:F.281, A:F.281, A:L.285, A:I.319, A:L.323, A:F.358, A:W.373, A:L.374, A:W.395, A:L.400, A:L.403, A:I.406 Hydrogen bonds: A:T.289, A:L.311, A:K.369 3PE.8: 14 residues within 4Å: Chain A: P.228, V.237, C.241, F.244, I.245, N.248, F.283, I.287, Y.290, H.313, Q.314, F.317 Chain B: A.231, W.232 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.244, A:F.283, A:I.287, A:Y.290, A:Y.290, A:F.317, B:W.232 Hydrogen bonds: A:H.313, A:Q.314 Salt bridges: A:H.313 3PE.17: 12 residues within 4Å: Chain A: I.249, T.250, K.258 Chain B: I.243, K.258, L.332, A.333, F.336, P.338 Ligands: 3PE.19, CLR.29, PLM.32 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.243, B:I.243, B:L.332, B:A.333, B:F.336, A:I.249, A:T.250 Salt bridges: B:K.258, B:K.258, A:K.258 3PE.19: 15 residues within 4Å: Chain A: I.243, K.258, L.329, L.332, A.333, F.336, A.337, P.338 Chain B: I.249, T.250, L.253, K.258 Ligands: CLR.6, PLM.9, 3PE.17 15 PLIP interactions: 9 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.243, A:I.243, A:L.329, A:L.332, A:A.333, A:P.338, B:I.249, B:I.249, B:T.250, B:K.258 Salt bridges: A:K.258, A:K.258, A:K.258, B:K.258, B:K.258 3PE.26: 21 residues within 4Å: Chain B: L.278, F.281, L.285, L.305, N.306, S.309, N.310, L.311, L.316, I.319, L.323, F.358, L.359, K.369, S.370, L.374, W.395, L.400, L.403, I.406, L.410 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:L.278, B:L.278, B:F.281, B:F.281, B:L.285, B:I.319, B:L.323, B:F.358, B:L.359, B:L.374, B:L.374, B:L.374, B:L.400, B:L.403, B:I.406, B:L.410 Hydrogen bonds: B:L.311, B:K.369, B:S.370 3PE.31: 15 residues within 4Å: Chain A: W.232, F.235 Chain B: Q.227, P.228, A.229, C.241, F.244, I.245, N.248, F.283, I.287, Y.290, H.313, Q.314, F.317 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.244, B:I.245, B:F.283, B:F.283, B:I.287, B:Y.290, B:Y.290, B:F.317, A:W.232, A:W.232, A:F.235 Hydrogen bonds: B:Q.227, B:A.229, B:Q.314 Salt bridges: B:H.313

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.9: 4 residues within 4Å: Chain A: W.232, F.235, R.236 Ligands: 3PE.19 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.235 Salt bridges: A:R.236 PLM.32: 5 residues within 4Å: Chain B: W.232, T.233, F.235, R.236 Ligands: 3PE.17 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.235 Salt bridges: B:R.236

2 x ACD: ARACHIDONIC ACID(Non-covalent)

ACD.11: 4 residues within 4Å: Chain A: I.265, W.266, I.591, P.598 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.265, A:W.266, A:W.266, A:I.591, A:P.598 ACD.34: 4 residues within 4Å: Chain B: I.265, W.266, I.591, P.598 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.265, B:W.266, B:W.266, B:I.591, B:P.598

10 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.12: 6 residues within 4Å: Chain A: N.401, K.482, T.486, T.525, R.570 Ligands: PO4.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.401, A:T.486, A:R.570 PO4.13: 7 residues within 4Å: Chain A: L.569, A.572, W.573, F.596, E.600 Ligands: PO4.14, PO4.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.573 PO4.14: 6 residues within 4Å: Chain A: R.570, E.600, R.603 Ligands: PO4.12, PO4.13, PO4.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.600 Salt bridges: A:R.570, A:R.603 PO4.15: 7 residues within 4Å: Chain A: M.489, Y.518, S.522, R.570, W.573 Ligands: PO4.13, PO4.14 No protein-ligand interaction detected (PLIP) PO4.16: 4 residues within 4Å: Chain A: Y.443, Q.452, M.489, W.573 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.452, A:Q.452, A:Q.452 PO4.20: 6 residues within 4Å: Chain B: N.401, K.482, Y.483, T.486, T.525 Ligands: PO4.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.401, B:K.482, B:T.525 PO4.21: 7 residues within 4Å: Chain B: M.489, Y.518, S.522, R.570, W.573 Ligands: PO4.22, PO4.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.522, B:R.570 PO4.22: 6 residues within 4Å: Chain B: R.570, E.600, R.603 Ligands: PO4.20, PO4.21, PO4.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.603 Salt bridges: B:R.570 PO4.23: 3 residues within 4Å: Chain B: Y.443, Q.452, W.573 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.443, B:Q.452 PO4.24: 6 residues within 4Å: Chain B: L.569, A.572, W.573, E.600 Ligands: PO4.21, PO4.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.569, B:A.572, B:W.573

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zuo, P. et al., Synergistic activation of the human phosphate exporter XPR1 by KIDINS220 and inositol pyrophosphate. Nat Commun (2025)

Release Date

2025-04-02

Peptides

Solute carrier family 53 member 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Membrane

We predict this structure to be a membrane protein.
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Solute carrier family 53 member 1

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