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8zto

Cryo-EM structure of the human XPR1

Method: ELECTRON MICROSCOPY Dmax: 116.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Solute carrier family 53 member 1

Homo sapiens

UniProt Q9UBH6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–696 Chain B； UniProt 1–696 Not recorded K9G [(2~{R})-1-hexadecanoyloxy-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propan-2-yl] octadec-9-enoate × 2 PO4 PHOSPHATE ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.55 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8ZTO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5IJH Structure of the SPX domain of the human phosphate transporter XPR1 in complex with a sulfate ion Deposited 2016-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–207（207 aa） Fragment：SPX domain, UNP Residues 1-207
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；1.4M AmSO4, 0.1M Tris, 16% glycerol
Resolution 2.43 Å R-free 0.244
5IJH Structure of the SPX domain of the human phosphate transporter XPR1 in complex with a sulfate ion Deposited 2016-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–207（207 aa） Fragment：SPX domain, UNP Residues 1-207
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；1.4M AmSO4, 0.1M Tris, 16% glycerol
Resolution 2.43 Å R-free 0.244
8TYU High-resolution crystal structure of the SPX domain of XPR1 at 1.4 angstroms Deposited 2023-08-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–94（94 aa） Fragment：SPX domain
Chain B 130–207（78 aa） Fragment：SPX domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；6% PEG 3350, 30% Ethylene Glycol, 0.1 M Sodium Citrate, 0.1 M MgCl2, pH 6.0.
Resolution 1.40 Å R-free 0.191
8TYU High-resolution crystal structure of the SPX domain of XPR1 at 1.4 angstroms Deposited 2023-08-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–94（94 aa） Fragment：SPX domain
Chain A 130–207（78 aa） Fragment：SPX domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；6% PEG 3350, 30% Ethylene Glycol, 0.1 M Sodium Citrate, 0.1 M MgCl2, pH 6.0.
Resolution 1.40 Å R-free 0.191
8TYV Crystal structure of the SPX domain of XPR1 in complex with IP8 Deposited 2023-08-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–94（94 aa） Fragment：SPX domain
Chain B 130–207（78 aa） Fragment：SPX domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；2mM IP8 soaked into crystals grown under 6% PEG 3350, 30% Ethylene Glycol, 0.1 M Sodium Citrate, 0.1 M MgCl2, pH 6.0 for 3 Days
Resolution 1.85 Å R-free 0.271
8TYV Crystal structure of the SPX domain of XPR1 in complex with IP8 Deposited 2023-08-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–94（94 aa） Fragment：SPX domain
Chain A 130–207（78 aa） Fragment：SPX domain
Not recorded I8P (1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)] × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；2mM IP8 soaked into crystals grown under 6% PEG 3350, 30% Ethylene Glycol, 0.1 M Sodium Citrate, 0.1 M MgCl2, pH 6.0 for 3 Days
Resolution 1.85 Å R-free 0.271
8X5B Cryo-EM structures of human XPR1 in closed states Deposited 2023-11-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 229–696（468 aa）
Chain F 229–696（468 aa）
Not recorded PO4 PHOSPHATE ION × 8 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 18 CLR CHOLESTEROL × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.84 Å
8X5E Cryo-EM structure of human XPR1 in open state Deposited 2023-11-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 229–696（468 aa）
Not recorded PO4 PHOSPHATE ION × 2 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 3.61 Å
8X5F human XPR1 in complex with InsP6 Deposited 2023-11-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded PO4 PHOSPHATE ION × 8 IHP INOSITOL HEXAKISPHOSPHATE × 2 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 30 CLR CHOLESTEROL × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
Resolution 2.96 Å
8YET Cryo EM structure of human phosphate channel XPR1 in complex with IP6 Deposited 2024-02-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–620（620 aa）
Chain B 1–620（620 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.16 Å
8YEX Cryo EM structure of human phosphate channel XPR1 at apo state Deposited 2024-02-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 228–619（392 aa）
Chain B 228–619（392 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.68 Å
8YF4 Cryo EM structure of human phosphate channel XPR1 at open and inward-facing state Deposited 2024-02-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 227–619（393 aa）
Chain B 227–619（393 aa）
Not recorded Y01 CHOLESTEROL HEMISUCCINATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.41 Å
8YFD Cryo EM structure of human phosphate channel XPR1 at open state Deposited 2024-02-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 227–622（396 aa）
Chain B 227–622（396 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.57 Å
8YFU Cryo EM structure of human phosphate channel XPR1 at intermediate state Deposited 2024-02-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 21–620（600 aa）
Chain B 21–620（600 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.59 Å
8YFW Cryo EM structure of human phosphate channel XPR1 at intermediate state Deposited 2024-02-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 21–620（600 aa）
Chain B 21–620（600 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.65 Å
8YFX Cryo EM structure of human phosphate channel XPR1 at inward-facing state Deposited 2024-02-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 227–622（396 aa）
Chain B 227–622（396 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.56 Å
9CKZ Cryo-EM structure of human XPR1 in apo state Deposited 2024-07-10 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
9CL0 Cryo-EM structure of human XPR1 in presence of inorganic phosphate and phytic acid Deposited 2024-07-10 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9DVJ "Structure of the phosphate exporter XPR1/SLC53A1 Deposited 2024-10-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded PO4 PHOSPHATE ION × 2 CLR CHOLESTEROL × 2 CPL 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.52 Å
9DVK Structure of the phosphate exporter XPR1/SLC53A1, rotated dimer Deposited 2024-10-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded PO4 PHOSPHATE ION × 2 CLR CHOLESTEROL × 1 CPL 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.06 Å
9DVL Structure of the phosphate exporter XPR1/SLC53A1, InsP6-supplemented Deposited 2024-10-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded PO4 PHOSPHATE ION × 6 CLR CHOLESTEROL × 2 CPL 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.97 Å
9DVM Structure of the phosphate exporter XPR1/SLC53A1, InsP8-bound, intracellular gate open/intracellular gate closed state Deposited 2024-10-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded PO4 PHOSPHATE ION × 6 I8P (1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)] × 4 CLR CHOLESTEROL × 2 CPL 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.92 Å
9DVN Structure of the phosphate exporter XPR1/SLC53A1, InsP8-bound, intracellular gate closed state Deposited 2024-10-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded PO4 PHOSPHATE ION × 6 I8P (1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)] × 4 CLR CHOLESTEROL × 2 CPL 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.75 Å
9DVO Structure of the phosphate exporter XPR1/SLC53A1, Pi and InsP8-bound, intracellular gate open/intracellular gate closed state Deposited 2024-10-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded PO4 PHOSPHATE ION × 4 I8P (1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)] × 4 CLR CHOLESTEROL × 2 CPL 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9DVP Structure of the phosphate exporter XPR1/SLC53A1, Pi and InsP8-bound, intracellular gate closed state Deposited 2024-10-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded PO4 PHOSPHATE ION × 5 I8P (1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)] × 4 CLR CHOLESTEROL × 2 CPL 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.81 Å
9IJY Homo sapiens Xenotropic and Polytropic Retrovirus Receptor 1 (XPR1) with Y22A/E23A/K26A mutations Deposited 2024-06-25 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Mutation：Y22A,E23A,K26A Mutation：Y22A,E23A,K26A PO4 PHOSPHATE ION × 2 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.64 Å
9IJZ Wild type Homo sapiens Xenotropic and Polytropic Retrovirus Receptor 1 (XPR1) Deposited 2024-06-25 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded PO4 PHOSPHATE ION × 2 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
9INE Cryo-EM structure of human XPR1 in closed state in the presence of KIDINS220-1-432 Deposited 2024-07-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded CLR CHOLESTEROL × 14 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 PLM PALMITIC ACID × 2 ACD ARACHIDONIC ACID × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
9INF Cryo-EM structure of human XPR1 in closed state in the presence of KIDINS220-1-432 and 10 mM KH2PO4 Deposited 2024-07-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded CLR CHOLESTEROL × 8 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6 PLM PALMITIC ACID × 2 ACD ARACHIDONIC ACID × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
9INH 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 Deposited 2024-07-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain D 1–696（696 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 2 CLR CHOLESTEROL × 12 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6 PLM PALMITIC ACID × 2 ACD ARACHIDONIC ACID × 2 PO4 PHOSPHATE ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.68 Å
9ITG Cryo-EM structure of human XPR1-E622A/F623A mutant in complex with InsP6 in inward-facing state in the presence of 10 mM KH2PO4 Deposited 2024-07-20 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Mutation：E622A, F623A Mutation：E622A, F623A PO4 PHOSPHATE ION × 2 IHP INOSITOL HEXAKISPHOSPHATE × 2 CLR CHOLESTEROL × 2 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 4 Y01 CHOLESTEROL HEMISUCCINATE × 2 PLM PALMITIC ACID × 2 1T9 (2S,3R,4E)-3-hydroxy-2-(octanoylamino)octadec-4-en-1-yl dihydrogen phosphate × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9IUC Cryo-EM structure of human XPR1 in complex with InsP6 in closed state - in the presence of KIDINS220-1-432 without substrate KH2PO4 Deposited 2024-07-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded CLR CHOLESTEROL × 12 IHP INOSITOL HEXAKISPHOSPHATE × 2 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6 PLM PALMITIC ACID × 4 ACD ARACHIDONIC ACID × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9IWS Cryo EM structure of human phosphate channel XPR1 in complex with IP7 Deposited 2024-07-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–631（631 aa）
Chain B 1–631（631 aa）
Not recorded I7P (1r,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.86 Å
9J4X CryoEM structure of human XPR1 in apo state Deposited 2024-08-10 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9J51 CryoEM structure of human XPR1 in complex with phosphate in state A Deposited 2024-08-11 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 4 PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9J52 CryoEM structure of human XPR1 in complex with phosphate in state B Deposited 2024-08-11 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 4 PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9J53 CryoEM structure of human XPR1 in complex with phosphate in state C Deposited 2024-08-11 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 4 PO4 PHOSPHATE ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9J97 Closed structure of human XPR1 Deposited 2024-08-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded 8PE (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate × 2 CLR CHOLESTEROL × 2 PO4 PHOSPHATE ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9J98 Open structure of human XPR1 Deposited 2024-08-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded 8PE (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate × 2 CLR CHOLESTEROL × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
9JXD Cryo-EM structure of human XPR1 in apo state Deposited 2024-10-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 230–625（396 aa）
Chain B 230–625（396 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.29 Å
9JXE Cryo-EM structure of apo human XPR1, class 1, with one visible SPX domain Deposited 2024-10-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–625（625 aa）
Chain B 1–625（625 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.85 Å
9JXF Cryo-EM structure of apo human XPR1, class 2, with asymmetrically dimerized SPX domains Deposited 2024-10-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: 12-meric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.31 Å
9JXG Cryo-EM structure of apo human XPR1, class 3, with symmetrically dimerized SPX domains Deposited 2024-10-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–696（696 aa）
Chain B 1–696（696 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.75 Å
9JXH Cryo-EM structure of human XPR1 in complex with InsP8 Deposited 2024-10-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–632（631 aa）
Chain B 2–632（631 aa）
Not recorded I8P (1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)] × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
9JXI Cryo-EM structure of human XPR1 with InsP8 in an 'arch-like' intermediate state of the SPX domain Deposited 2024-10-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–624（623 aa）
Chain B 2–624（623 aa）
Not recorded I8P (1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)] × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å
9JXJ Cryo-EM structure of human XPR1 in a closed state at both the extracellular and intracellular gates, obtained through local refinement Deposited 2024-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–624（624 aa）
Not recorded PO4 PHOSPHATE ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
9JXK Cryo-EM structure of human XPR1 in a closed state at the intracellular gate and an open state at the extracellular gate, obtained through local refinement Deposited 2024-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–625（625 aa）
Not recorded PO4 PHOSPHATE ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
9JXL Cryo-EM structure of human XPR1 in an open state at the intracellular gate and a closed state at the extracellular gate, obtained through local refinement Deposited 2024-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–632（632 aa）
Not recorded PO4 PHOSPHATE ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
9JXM Cryo-EM structure of one subunit of the human XPR1 homodimer with both the intracellular and extracellular gates in an open state, obtained through local refinement Deposited 2024-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–632（632 aa）
Not recorded PO4 PHOSPHATE ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.48 Å
9JXN Cryo-EM structure of human XPR1-R459C Deposited 2024-10-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–634（633 aa）
Chain B 2–634（633 aa）
Mutation：R459C Mutation：R459C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9JXO Cryo-EM structure of human XPR1-G621A Deposited 2024-10-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–632（631 aa）
Chain B 2–632（631 aa）
Mutation：G621A Mutation：G621A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.48 Å
9JXP Cryo-EM structure of human XPR1-R570L Deposited 2024-10-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 230–625（396 aa）
Chain B 230–625（396 aa）
Mutation：R570L Mutation：R570L No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.53 Å
9JXQ Complex of XPR1-KIDINS220 Deposited 2024-10-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–655（655 aa）
Chain B 1–655（655 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å

50 other PDB entries and 53 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name S53A1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–696； UniProt 1–696 Author chain B； PDBConstruct 1–696； UniProt 1–696

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8zto

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8zto
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8zto
Deposition date deposition_date2024-06-07
Structure title titleCryo-EM structure of the human XPR1
Keywords keywordsSLC transporter, XPR1, SLC53A1, structural protein, Pi, exporter; STRUCTURAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.96 Å
Radius of gyration Rg (electron density) rg_electron34.11 Å
Forward intensity I(0) i0107672000.00
Molecular weight molecular_weight92908.0 kDa
Excluded volume excluded_volume120220 ų
Envelope volume envelope_volume153540 ų
Hydration-shell volume shell_volume38052 ų
Envelope diameter envelope_diameter115.4 Å
Shell Rg shell_rg39.78 Å
Envelope Rg envelope_rg33.99 Å
Shape Rg shape_rg34.10 Å
Total Rg total_rg34.63 Å
Total atoms total_atoms6590
Residues n_residues778
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax116.1 Å
Rg (real space) rg_real35.05 Å
Rg uncertainty (real space) rg_real_error1.14 Å
I(0) (real space) i0_real1.0770e+08
I(0) uncertainty (real space) i0_real_error1.8680e+06
Rg (reciprocal space) rg_reciprocal34.99 Å
I(0) (reciprocal space) i0_reciprocal107700000.0000
Solution quality estimate total_estimate0.8849
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.5 Å
Skewness Skewness skewness0.308
Kurtosis Kurtosis kurtosis-0.650
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9362000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.914; Smooth: 0.899
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)