9dvk

Structure of the phosphate exporter XPR1/SLC53A1, rotated dimer

Method: ELECTRON MICROSCOPY D_max: 109.4 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

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	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

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 9DVK	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
8ZTO Cryo-EM structure of the human XPR1 Deposited 2024-06-07	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	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
9CKZ Cryo-EM structure of human XPR1 in apo state Deposited 2024-07-10	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	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 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 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
9DVL Structure of the phosphate exporter XPR1/SLC53A1, InsP6-supplemented Deposited 2024-10-08	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	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 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 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 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 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 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 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 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	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 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	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 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	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 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	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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9dvk
Deposition date deposition_date	2024-10-08
Structure title title	Structure of the phosphate exporter XPR1/SLC53A1, rotated dimer
Keywords keywords	Inorganic phosphate exporter, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	34.23 Å
Radius of gyration Rg (electron density) rg_electron	33.17 Å
Forward intensity I(0) i0	102090000.00
Molecular weight molecular_weight	91924.0 kDa
Excluded volume excluded_volume	119500 Å³
Envelope volume envelope_volume	143740 Å³
Hydration-shell volume shell_volume	36812 Å³
Envelope diameter envelope_diameter	116.7 Å
Shell Rg shell_rg	39.12 Å
Envelope Rg envelope_rg	32.88 Å
Shape Rg shape_rg	33.16 Å
Total Rg total_rg	33.73 Å
Total atoms total_atoms	13112
Residues n_residues	760
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	109.4 Å
Rg (real space) rg_real	34.31 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	1.0210e+08
I(0) uncertainty (real space) i0_real_error	1.6380e+06
Rg (reciprocal space) rg_reciprocal	34.26 Å
I(0) (reciprocal space) i0_reciprocal	102100000.0000
Solution quality estimate total_estimate	0.8905
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	33.3 Å
Skewness Skewness skewness	0.286
Kurtosis Kurtosis kurtosis	-0.730
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7623000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.879

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Solute carrier family 53 member 1
Molecular weight formula_weight	82364.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	13112

MKFAEHLSAHITPEWRKQYIQYEAFKDMLYSAQDQAPSVEVTDEDTVKRYFAKFEEKFFQTCEKELAKINTFYSEKLAEAQRRFATLQNELQSSLDAQKESTGVTTLRQRRKPVFHLSHEERVQHRNIKDLKLAFSEFYLSLILLQNYQNLNFTGFRKILKKHDKILETSRGADWRVAHVEVAPFYTCKKINQLISETEAVVTNELEDGDRQKAMKRLRVPPLGAAQPAPAWTTFRVGLFCGIFIVLNITLVLAAVFKLETDRSIWPLIRIYRGGFLLIEFLFLLGINTYGWRQAGVNHVLIFELNPRSNLSHQHLFEIAGFLGILWCLSLLACFFAPISVIPTYVYPLALYGFMVFFLINPTKTFYYKSRFWLLKLLFRVFTAPFHKVGFADFWLADQLNSLSVILMDLEYMICFYSLELKWDESKGLLPNNSEESGICHKYTYGVRAIVQCIPAWLRFIQCLRRYRDTKRAFPHLVNAGKYSTTFFMVTFAALYSTHKERGHSDTMVFFYLWIVFYIISSCYTLIWDLKMDWGLFDKNAGENTFLREEIVYPQKAYYYCAIIEDVILRFAWTIQISITSTTLLPHSGDIIATVFAPLEVFRRFVWNFFRLENEHLNNCGEFRAVRDISVAPLNADDQTLLEQMMDQDDGVRNRQKNRSWKYNQSISLRRPRLASQSKARDTKVLIEDTDDEANTLEVLFQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHOLESTEROL
Molecular weight formula_weight	386.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Molecular weight formula_weight	758.1 kDa
Source method src_method	syn
Copy count entity_count	3

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.060 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.06 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	124969

fit	/app/data/saxs_computation/dv/9dvk/9dvk.fit
pddf	/app/data/pr_computation/dv/9dvk/9dvk.pr.out
profile	/app/data/saxs_computation/dv/9dvk/9dvk.dat