SMTL ID : 9itg.1

Cryo-EM structure of human XPR1-E622A/F623A mutant in complex with InsP6 in inward-facing state in the presence of 10 mM KH2PO4

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.03 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: F.394, D.398, R.459, N.479, K.482, Y.483, D.533, W.607 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.479, A:Y.483, A:Y.483, A:D.533, A:D.533 Salt bridges: A:R.459, A:K.482 PO4.9: 8 residues within 4Å: Chain B: F.394, D.398, R.459, K.482, Y.483, W.528, D.533, W.607 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.398, B:Y.483, B:D.533, B:D.533 Salt bridges: B:R.459, B:K.482

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.2: 11 residues within 4Å: Chain A: M.1, F.3, Y.22, Y.30, K.158, K.161, K.162, K.165 Chain B: R.211, M.215, R.219 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:M.1, A:M.1, A:F.3, A:Y.30 Water bridges: A:K.162, A:K.162 Salt bridges: A:K.2, A:K.158, A:K.161, A:K.161, A:K.161, A:K.162, A:K.162, A:K.165, A:K.165, A:K.165, B:R.219 IHP.10: 12 residues within 4Å: Chain A: R.211, M.215, R.219 Chain B: M.1, K.2, F.3, Y.22, Y.30, K.158, K.161, K.162, K.165 19 PLIP interactions: 17 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:M.1, B:M.1, B:M.1, B:F.3, B:Y.30, A:R.219 Water bridges: B:K.162, B:K.162 Salt bridges: B:K.2, B:K.158, B:K.161, B:K.161, B:K.161, B:K.162, B:K.162, B:K.165, B:K.165, B:K.165, A:R.219

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.3: 8 residues within 4Å: Chain A: Y.558, C.561, A.562, E.565, F.605, V.606, F.609 Ligands: PLM.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.558, A:A.562, A:E.565, A:F.605, A:V.606, A:V.606, A:F.609 CLR.11: 8 residues within 4Å: Chain B: Y.558, C.561, A.562, E.565, F.605, V.606, F.609 Ligands: PLM.15 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.558, B:A.562, B:E.565, B:F.605, B:V.606, B:V.606, B:F.609

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

3PE.4: 15 residues within 4Å: Chain A: L.278, F.281, L.282, L.285, L.305, N.306, S.309, N.310, L.311, Y.352, M.355, L.359, S.370, W.373, L.374 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.278, A:L.282, A:L.282, A:L.285, A:Y.352, A:M.355, A:L.359, A:L.359, A:W.373, A:L.374, A:L.374 Hydrogen bonds: A:L.311 3PE.5: 18 residues within 4Å: Chain A: I.243, L.247, K.258, L.326, L.329, S.330, L.332, A.333, F.336, A.337, P.338, S.340, Y.347, A.350, L.351 Chain B: V.246, F.257 Ligands: 3PE.13 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.243, A:L.247, A:L.329, A:L.329, A:L.332, A:A.333, A:F.336, A:F.336, A:P.338, A:A.350, A:L.351, A:L.351, B:V.246, B:F.257 Hydrogen bonds: A:A.337 Salt bridges: A:K.258, A:K.258, A:K.258 3PE.12: 15 residues within 4Å: Chain B: L.278, F.281, L.282, L.285, L.305, N.306, S.309, N.310, L.311, Y.352, M.355, L.359, S.370, W.373, L.374 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.278, B:L.282, B:L.282, B:L.285, B:Y.352, B:M.355, B:L.359, B:L.359, B:W.373, B:L.374, B:L.374 Hydrogen bonds: B:L.311 3PE.13: 18 residues within 4Å: Chain A: V.246, F.257 Chain B: I.243, L.247, K.258, L.326, L.329, S.330, L.332, A.333, F.336, A.337, P.338, S.340, Y.347, A.350, L.351 Ligands: 3PE.5 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.243, B:L.247, B:L.329, B:L.329, B:A.333, B:F.336, B:F.336, B:P.338, B:A.350, B:L.351, B:L.351, A:V.246, A:F.257 Hydrogen bonds: B:A.337 Salt bridges: B:K.258, B:K.258, B:K.258

2 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.6: 8 residues within 4Å: Chain A: F.474, I.520, C.523, Y.524, I.527, W.528, K.531, M.532 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.474, A:F.474, A:I.520, A:Y.524, A:Y.524, A:Y.524, A:I.527, A:W.528, A:W.528, A:K.531 Salt bridges: A:K.531 Y01.14: 8 residues within 4Å: Chain B: F.474, I.520, C.523, Y.524, I.527, W.528, K.531, M.532 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.474, B:F.474, B:I.520, B:Y.524, B:Y.524, B:Y.524, B:I.527, B:W.528, B:W.528 Salt bridges: B:K.531

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.7: 7 residues within 4Å: Chain A: E.280, L.284, Y.290, P.598, F.602, F.605 Ligands: CLR.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.284, A:F.602, A:F.602, A:F.605 PLM.15: 7 residues within 4Å: Chain B: E.280, L.284, Y.290, P.598, F.602, F.605 Ligands: CLR.11 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.284, B:F.602, B:F.602, B:F.605

2 x 1T9: (2S,3R,4E)-3-hydroxy-2-(octanoylamino)octadec-4-en-1-yl dihydrogen phosphate(Non-covalent)

1T9.8: 11 residues within 4Å: Chain A: C.241, F.244, I.279, F.283, Y.290, H.313, Q.314, F.317, G.321 Chain B: W.232, F.235 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.244, A:I.279, A:F.283, A:F.283, A:Y.290, A:F.317, A:F.317, A:F.317, B:W.232, B:F.235 Hydrogen bonds: A:H.313, A:Q.314 1T9.16: 12 residues within 4Å: Chain A: A.231, W.232, F.235 Chain B: C.241, F.244, I.279, F.283, Y.290, H.313, Q.314, F.317, G.321 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.244, B:I.279, B:F.283, B:F.283, B:Y.290, B:F.317, B:F.317, B:F.317, A:W.232, A:F.235 Hydrogen bonds: B:H.313, B:Q.314

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