SMTL ID : 9dvo.1

Structure of the phosphate exporter XPR1/SLC53A1, Pi and InsP8-bound, intracellular gate open/intracellular gate closed state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.10 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: V.389, F.394, R.459, C.463, R.466, H.476, N.479, R.611 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.479 Salt bridges: A:R.459, A:R.466 PO4.2: 8 residues within 4Å: Chain A: D.398, N.401, S.402, R.570, W.573, E.600, R.603, R.604 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.402, A:S.402, A:S.402 Salt bridges: A:R.570, A:R.603, A:R.604 PO4.3: 7 residues within 4Å: Chain A: R.270, M.408, D.409, E.411, Y.412, R.448, T.580 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.409, A:D.409, A:Y.412 Salt bridges: A:R.270, A:R.448 PO4.8: 10 residues within 4Å: Chain B: V.389, F.394, R.459, C.463, R.466, H.476, N.479, R.611, G.621, F.623 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.479 Salt bridges: B:R.459, B:R.466, B:H.476

4 x I8P: (1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)](Non-covalent)

I8P.4: 16 residues within 4Å: Chain A: M.1, K.2, F.3, A.4, E.5, Y.22, K.26, Y.30, R.157, K.158, K.161, K.162, K.165 Chain B: R.211, M.215, R.219 25 PLIP interactions: 22 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:M.1, A:K.2, A:F.3, A:A.4, A:Y.22, A:Y.22, B:R.211 Water bridges: A:K.161, A:K.161 Salt bridges: A:K.26, A:R.157, A:K.158, A:K.158, A:K.161, A:K.161, A:K.161, A:K.161, A:K.162, A:K.162, A:K.162, A:K.165, A:K.165, A:K.165, B:R.219, B:R.219 I8P.5: 6 residues within 4Å: Chain A: K.129, K.213, R.217, K.364, Y.368, K.369 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.217, A:Y.368 Salt bridges: A:K.129, A:K.129, A:K.364, A:K.364, A:K.369, A:K.369 I8P.9: 15 residues within 4Å: Chain A: R.211, Q.212, M.215, R.219 Chain B: M.1, K.2, F.3, A.4, Y.22, K.26, R.157, K.158, K.161, K.162, K.165 20 PLIP interactions: 2 interactions with chain A, 18 interactions with chain B Hydrogen bonds: A:R.211, B:M.1, B:F.3, B:A.4 Salt bridges: A:R.219, B:K.26, B:R.157, B:K.158, B:K.161, B:K.161, B:K.161, B:K.161, B:K.162, B:K.162, B:K.162, B:K.165, B:K.165, B:K.165 Water bridges: B:K.161, B:K.161 I8P.10: 10 residues within 4Å: Chain B: H.125, K.129, K.132, L.133, K.216, R.217, K.364, Y.368, K.369 Ligands: CPL.12 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:H.125 Salt bridges: B:K.129, B:K.129, B:K.129, B:K.129, B:K.132, B:K.216, B:R.217, B:K.364, B:K.364, B:K.369, B:K.369

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 16 residues within 4Å: Chain A: I.287, G.291, Q.294, A.295, Y.553, Y.558, C.561, A.562, I.564, E.565, I.568, F.602, F.605, V.606, F.609, F.610 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.558, A:E.565, A:F.602, A:F.605, A:F.605, A:F.609, A:F.609 CLR.11: 17 residues within 4Å: Chain B: I.287, Y.290, G.291, Q.294, A.295, Y.553, P.554, Y.558, C.561, A.562, I.564, E.565, F.602, F.605, V.606, F.609, F.610 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.605, B:V.606

2 x CPL: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

CPL.7: 35 residues within 4Å: Chain A: L.278, F.281, L.282, L.285, T.289, W.292, H.299, F.303, L.305, N.306, S.309, N.310, L.311, L.316, I.319, L.323, Y.352, M.355, V.356, F.358, L.359, K.369, S.370, R.371, W.373, L.374, L.377, L.378, W.395, L.396, L.400, L.403, I.406, L.407, L.410 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.278, A:F.281, A:F.303, A:F.303, A:Y.352, A:M.355, A:V.356, A:L.359, A:L.359, A:L.359, A:W.373, A:L.374, A:L.374, A:L.374, A:W.395, A:W.395, A:L.396, A:L.400, A:L.400, A:L.403 Hydrogen bonds: A:S.309, A:L.311, A:S.370 CPL.12: 37 residues within 4Å: Chain B: L.278, F.281, L.282, L.285, T.289, W.292, H.299, F.303, L.305, N.306, S.309, N.310, L.311, L.316, I.319, L.323, Y.352, M.355, V.356, F.358, L.359, K.369, S.370, R.371, W.373, L.374, K.376, L.377, L.378, W.395, L.396, Q.399, L.400, L.403, I.406, L.407 Ligands: I8P.10 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.278, B:F.281, B:L.285, B:F.303, B:L.316, B:I.319, B:F.358, B:L.359, B:L.359, B:L.374, B:L.374, B:W.395, B:L.396, B:L.400, B:I.406, B:I.406 Hydrogen bonds: B:S.309, B:L.311

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, Q. et al., Transport and InsP 8 gating mechanisms of the human inorganic phosphate exporter XPR1. 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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