SMTL ID : 9ine.1

Cryo-EM structure of human XPR1 in closed state in the presence of KIDINS220-1-432

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

14 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, V.606, F.609 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.553, A:Y.558, A:Y.558, A:E.565, A:E.565, A:F.602, A:F.605, A:V.606, A:F.609 CLR.4: 8 residues within 4Å: Chain A: G.446, I.450, W.457, F.460, F.487, T.491, A.494, T.498 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.450, A:I.450, A:W.457, A:F.460, A:F.487, A:F.487, A:A.494 CLR.5: 5 residues within 4Å: Chain A: P.338 Chain B: L.253, F.257 Ligands: 3PE.3, LPE.10 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.253, B:F.257 CLR.6: 3 residues within 4Å: Chain A: F.511, I.515, I.519 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.511, A:I.515, A:I.519 CLR.8: 7 residues within 4Å: Chain A: I.520, C.523, Y.524, I.527, W.528, K.531, M.532 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.524, A:Y.524, A:I.527, A:W.528 CLR.9: 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:L.477, A:V.478, A:T.485, A:F.488, A:F.517, A:I.520 CLR.12: 5 residues within 4Å: Chain A: L.349, V.356, Y.417, S.418, W.423 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.356, A:Y.417, A:W.423 CLR.15: 9 residues within 4Å: Chain B: Y.553, Y.558, C.561, E.565, I.568, F.602, F.605, V.606, F.609 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.553, B:Y.558, B:Y.558, B:E.565, B:I.568, B:F.602, B:F.605, B:V.606, B:F.609 CLR.17: 8 residues within 4Å: Chain B: G.446, A.449, I.450, W.457, F.460, F.487, T.491, A.494 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.449, B:W.457, B:F.460, B:F.487, B:F.487, B:T.491, B:A.494 CLR.18: 6 residues within 4Å: Chain A: L.253, F.257 Chain B: P.338, S.340 Ligands: 3PE.14, LPE.23 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.253, A:F.257 Hydrogen bonds: B:S.340 CLR.19: 4 residues within 4Å: Chain B: F.511, I.515, I.519, F.571 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.511, B:I.515, B:I.519, B:F.571 CLR.21: 7 residues within 4Å: Chain B: I.520, C.523, Y.524, I.527, W.528, K.531, M.532 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.524, B:Y.524, B:I.527, B:W.528 CLR.22: 9 residues within 4Å: Chain B: 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 B Hydrophobic interactions: B:L.477, B:V.478, B:T.485, B:F.488, B:F.517, B:I.520 CLR.25: 4 residues within 4Å: Chain B: L.349, Y.417, S.418, W.423 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.417, B:W.423

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

3PE.2: 25 residues within 4Å: Chain A: L.278, F.281, L.282, L.285, T.289, H.299, F.303, L.305, N.306, S.309, N.310, L.311, L.316, L.323, Y.352, M.355, 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:L.282, A:L.285, A:F.303, A:L.323, A:Y.352, A:M.355, A:L.359, A:W.373, A:W.373, A:L.374, 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, T.250, L.326, L.329, L.332, A.333, F.336, P.338, Y.347, L.351, F.354 Chain B: I.249, T.250, L.253, F.257 Ligands: CLR.5, LPE.10, PLM.11, 3PE.14 16 PLIP interactions: 4 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:I.249, B:I.249, B:T.250, B:L.253, A:I.243, A:I.243, A:T.250, A:L.326, A:L.329, A:L.332, A:A.333, A:F.336, A:F.336, A:P.338, A:Y.347, A:F.354 3PE.7: 15 residues within 4Å: Chain A: P.228, A.229, C.241, F.244, N.248, I.249, F.283, I.287, Y.290, H.313, Q.314, F.317 Chain B: A.231, W.232, F.235 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.244, A:I.249, A:F.283, A:I.287, A:Y.290, A:Y.290, B:W.232 Hydrogen bonds: A:A.229, A:Q.314 Salt bridges: A:H.313 3PE.14: 19 residues within 4Å: Chain A: I.249, T.250, L.253, F.257 Chain B: I.243, T.250, L.326, L.329, L.332, A.333, F.336, P.338, Y.347, L.351, F.354 Ligands: 3PE.3, CLR.18, LPE.23, PLM.24 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.243, B:I.243, B:T.250, B:L.326, B:L.329, B:L.332, B:A.333, B:F.336, B:F.336, B:P.338, B:Y.347, B:F.354, A:I.249, A:I.249, A:T.250, A:L.253 3PE.16: 23 residues within 4Å: Chain B: L.278, F.281, L.285, T.289, H.299, F.303, L.305, N.306, S.309, N.310, L.311, L.323, Y.352, M.355, 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 B Hydrophobic interactions: B:L.278, B:L.285, B:F.303, B:L.323, B:Y.352, B:M.355, B:L.359, B:L.359, B:W.373, B:W.373, B:L.374, B:L.374, B:W.395, B:W.395, B:L.400, B:I.406, B:L.410 Hydrogen bonds: B:K.369 Salt bridges: B:H.299 3PE.20: 15 residues within 4Å: Chain A: A.231, W.232, F.235 Chain B: P.228, A.229, C.241, F.244, N.248, I.249, F.283, I.287, Y.290, H.313, Q.314, F.317 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.244, B:I.249, B:F.283, B:I.287, B:Y.290, B:Y.290, A:W.232 Hydrogen bonds: B:A.229, B:Q.314 Salt bridges: B:H.313

2 x LPE: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

LPE.10: 14 residues within 4Å: Chain A: R.236, L.239, F.240, E.318, F.322, I.325, L.329, F.354, T.365, F.366, Y.367 Ligands: 3PE.3, CLR.5, PLM.11 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.239, A:F.240, A:I.325, A:L.329, A:F.354 Salt bridges: A:R.236, A:E.318 pi-Cation interactions: A:F.322, A:F.366 LPE.23: 14 residues within 4Å: Chain B: R.236, L.239, F.240, E.318, F.322, I.325, L.329, F.354, T.365, F.366, Y.367 Ligands: 3PE.14, CLR.18, PLM.24 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.239, B:F.240, B:I.325, B:L.329, B:F.354 Salt bridges: B:R.236, B:E.318 pi-Cation interactions: B:F.322, B:F.366

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.11: 6 residues within 4Å: Chain A: W.232, F.235, R.236 Chain B: I.245 Ligands: 3PE.3, LPE.10 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.232, A:F.235, B:I.245 Salt bridges: A:R.236 PLM.24: 6 residues within 4Å: Chain A: I.245 Chain B: W.232, F.235, R.236 Ligands: 3PE.14, LPE.23 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.232, B:F.235, A:I.245 Salt bridges: B:R.236

2 x ACD: ARACHIDONIC ACID(Non-covalent)

ACD.13: 5 residues within 4Å: Chain A: R.263, S.264, I.265, W.266, P.598 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.265, A:P.598 ACD.26: 5 residues within 4Å: Chain B: R.263, S.264, W.266, P.598, L.599 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.598, B:L.599

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
B

B
A

Membrane

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

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