SMTL ID : 9inf.1

Cryo-EM structure of human XPR1 in closed state in the presence of KIDINS220-1-432 and 10 mM KH2PO4

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

8 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 8 residues within 4Å: Chain A: Y.553, Y.558, C.561, E.565, F.602, F.605, F.609, F.610 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.553, A:Y.558, A:E.565, A:F.602, A:F.605, A:F.609, A:F.609, A:F.610 CLR.4: 10 residues within 4Å: Chain A: T.444, Y.445, G.446, A.449, I.450, C.453, W.457, F.487, T.491, A.494 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.450, A:I.450, A:F.487, A:A.494 CLR.5: 5 residues within 4Å: Chain A: P.338, I.339 Chain B: L.253, F.257 Ligands: 3PE.3 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.338, A:I.339, B:L.253, B:F.257 CLR.7: 6 residues within 4Å: Chain A: F.474, V.478, I.520, Y.524, I.527, K.531 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.474, A:V.478, A:I.520, A:Y.524, A:I.527, A:K.531 CLR.8: 9 residues within 4Å: Chain A: A.473, L.477, V.478, G.481, T.485, F.488, F.517, I.520, Y.524 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.473, A:L.477, A:V.478, A:F.488, A:F.517, A:I.520 CLR.11: 7 residues within 4Å: Chain B: Y.558, C.561, E.565, F.602, F.605, V.606, F.609 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.558, B:E.565, B:F.602, B:F.605, B:V.606 CLR.14: 4 residues within 4Å: Chain A: L.253 Chain B: P.338, I.339 Ligands: 3PE.13 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.339, A:L.253 CLR.16: 5 residues within 4Å: Chain B: F.474, I.520, C.523, Y.524, I.527 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.474, B:Y.524, B:I.527

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

3PE.2: 23 residues within 4Å: Chain A: L.278, F.281, L.282, L.285, T.289, L.305, N.306, S.309, N.310, L.311, L.323, Y.352, M.355, F.358, L.359, K.369, S.370, W.373, L.374, W.395, L.400, I.406, L.410 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.278, A:F.281, A:L.282, A:L.323, A:Y.352, A:Y.352, A:M.355, A:F.358, A:L.359, A:L.359, A:W.373, A:L.374, A:W.395, A:W.395, A:L.400, A:I.406, A:L.410 Hydrogen bonds: A:K.369 Salt bridges: A:H.299 3PE.3: 19 residues within 4Å: Chain A: I.243, L.247, T.250, K.258, L.326, L.329, L.332, A.333, F.336, P.338, A.350, L.351, F.354 Chain B: V.246, I.249, T.250, F.257 Ligands: CLR.5, 3PE.13 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.243, A:L.247, A:T.250, A:L.326, A:L.329, A:L.332, A:F.336, A:A.350, A:F.354, B:V.246, B:I.249, B:I.249, B:T.250, B:F.257 Salt bridges: A:K.258, A:K.258, A:K.258 3PE.6: 18 residues within 4Å: Chain A: Q.227, P.228, A.229, T.234, 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, F.235 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.244, A:I.245, A:N.248, A:F.283, A:I.287, A:Y.290, A:Y.290, A:Y.290, B:W.232, B:F.235 Hydrogen bonds: A:Q.227, A:A.229, A:Q.314 Salt bridges: A:H.313 3PE.12: 28 residues within 4Å: Chain B: L.278, F.281, L.282, L.285, T.289, F.303, L.305, N.306, S.309, N.310, L.311, L.316, I.319, L.323, Y.352, M.355, F.358, L.359, K.369, S.370, W.373, L.374, W.395, L.396, L.400, L.403, I.406, L.410 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:L.278, B:F.281, B:L.282, B:F.303, B:I.319, B:L.323, B:Y.352, B:Y.352, B:M.355, B:F.358, B:L.359, B:W.373, B:L.374, B:L.374, B:W.395, B:W.395, B:L.396, B:L.400, B:L.403, B:I.406, B:L.410 Hydrogen bonds: B:N.306, B:N.306 3PE.13: 19 residues within 4Å: Chain A: V.246, T.250, L.253, F.257 Chain B: I.243, L.247, T.250, K.258, L.326, L.329, L.332, A.333, F.336, P.338, Y.347, F.354 Ligands: 3PE.3, CLR.14, PLM.17 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.243, B:T.250, B:L.326, B:L.332, B:F.336, B:Y.347, B:F.354, A:V.246, A:V.246, A:L.253, A:F.257 Salt bridges: B:K.258, B:K.258, B:K.258 3PE.15: 16 residues within 4Å: Chain A: A.231, W.232, F.235 Chain B: A.229, C.241, F.244, I.245, N.248, I.249, F.283, I.287, Y.290, R.293, H.313, Q.314, F.317 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.244, B:I.245, B:N.248, B:I.249, B:F.283, B:F.283, B:I.287, B:Y.290, B:Y.290, B:F.317, B:F.317, A:W.232, A:F.235 Hydrogen bonds: B:A.229, B:R.293, B:Q.314 Salt bridges: B:H.313

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.9: 5 residues within 4Å: Chain A: W.232, T.233, F.235, R.236 Chain B: I.245 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.232, A:W.232, A:W.232, A:F.235, B:I.245 Hydrogen bonds: A:T.233 Salt bridges: A:R.236 PLM.17: 5 residues within 4Å: Chain A: I.245 Chain B: W.232, F.235, R.236 Ligands: 3PE.13 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.245, B:W.232, B:F.235 Salt bridges: B:R.236

2 x ACD: ARACHIDONIC ACID(Non-covalent)

ACD.10: 7 residues within 4Å: Chain A: S.264, I.265, W.266, H.587, I.591, P.598, L.599 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.265, A:I.265, A:I.591, A:L.599 Salt bridges: A:H.587 ACD.18: 6 residues within 4Å: Chain B: T.261, R.263, I.265, I.591, P.598, L.599 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.265, B:I.591, B:P.598, B:L.599 Salt bridges: B:H.587

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
B

Membrane

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

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