SAXSdb — 7yu4

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Lysophosphatidic acid receptor 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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2–364	Not recorded	K6L [(2~{R})-2-[5-(2-hexylphenyl)pentanoylamino]-3-oxidanyl-propyl] dihydrogen phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.70 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 7YU4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4Z34 Crystal Structure of Human Lysophosphatidic Acid Receptor 1 in complex with ONO9780307 Deposited 2015-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–232（231 aa） Fragment：unp residues 2-232; unp residues 23-64; unp residues 73-127; unp residues 248-326 Chain A 248–326（79 aa） Fragment：unp residues 2-232; unp residues 23-64; unp residues 73-127; unp residues 248-326	Mutation：M1007W, H1102I, R1106L Mutation：M1007W, H1102I, R1106L	ON7 {1-[(2S,3S)-2-(2,3-dihydro-1H-inden-2-ylmethyl)-3-(3,5-dimethoxy-4-methylphenyl)-3-hydroxypropyl]-4-(methoxycarbonyl)-1 H-pyrrol-3-yl}acetic acid × 1 1WV (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5.5；293 K；0.1 M sodium citrate (pH 5.5), 34 - 38% (v/v) PEG400 and 200 mM ammonium acetate	Resolution 3.00 Å R-free 0.281
4Z35 Crystal Structure of Human Lysophosphatidic Acid Receptor 1 in complex with ONO-9910539 Deposited 2015-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–232（231 aa） Chain A 248–326（79 aa）	Mutation：M1007W, H1102I, R1106L Mutation：M1007W, H1102I, R1106L	ON9 3-{1-[(2S,3S)-3-(4-acetyl-3,5-dimethoxyphenyl)-2-(2,3-dihydro-1H-inden-2-ylmethyl)-3-hydroxypropyl]-4-(methoxycarbonyl)-1H-pyrrol-3-yl}propanoic acid × 1 1WV (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5.5；293 K；0.1 M sodium citrate (pH 5.5), 34 - 38% (v/v) PEG400 and 200 mM ammonium acetate	Resolution 2.90 Å R-free 0.279
4Z36 Crystal Structure of Human Lysophosphatidic Acid Receptor 1 in complex with ONO-3080573 Deposited 2015-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–232（231 aa） Fragment：unp residues 2-232; unp residues 23-64; unp residues 78-127; unp residues 249-327 Chain A 249–327（79 aa） Fragment：unp residues 2-232; unp residues 23-64; unp residues 78-127; unp residues 249-327	Mutation：M1007W, H1102I, R1106L Mutation：M1007W, H1102I, R1106L	ON3 1-(4-{[(2S,3R)-2-(2,3-dihydro-1H-inden-2-yloxy)-3-(3,5-dimethoxy-4-methylphenyl)-3-hydroxypropyl]oxy}phenyl)cyclopropan ecarboxylic acid × 1 1WV (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5.5；293 K；0.1 M sodium citrate (pH 5.5), 34 - 38% (v/v) PEG400 and 200 mM ammonium acetate	Resolution 2.90 Å R-free 0.292
7TD0 Lysophosphatidic acid receptor 1-Gi complex bound to LPA Deposited 2021-12-30	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 R 2–340（339 aa）	Not recorded	NKP (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.83 Å
7TD1 Lysophosphatidic acid receptor 1-Gi complex bound to LPA, state a Deposited 2021-12-30	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 R 2–340（339 aa）	Not recorded	NKP (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.08 Å
7TD2 Lysophosphatidic acid receptor 1-Gi complex bound to LPA, state a Deposited 2021-12-30	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 R 2–340（339 aa）	Not recorded	NKP (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.11 Å
7YU3 Human Lysophosphatidic Acid Receptor 1-Gi complex bound to ONO-0740556 Deposited 2022-08-16	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 2–364（363 aa）	Not recorded	K6L [(2~{R})-2-[5-(2-hexylphenyl)pentanoylamino]-3-oxidanyl-propyl] dihydrogen phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7YU5 Human Lysophosphatidic Acid Receptor 1-Gi complex bound to ONO-0740556, state1 Deposited 2022-08-16	Different oligomeric state	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 2–364（363 aa）	Not recorded	K6L [(2~{R})-2-[5-(2-hexylphenyl)pentanoylamino]-3-oxidanyl-propyl] dihydrogen phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
7YU6 Human Lysophosphatidic Acid Receptor 1-Gi complex bound to ONO-0740556, state2 Deposited 2022-08-16	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 2–364（363 aa）	Not recorded	K6L [(2~{R})-2-[5-(2-hexylphenyl)pentanoylamino]-3-oxidanyl-propyl] dihydrogen phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7YU7 Human Lysophosphatidic Acid Receptor 1-Gi complex bound to ONO-0740556, state3 Deposited 2022-08-16	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 2–364（363 aa）	Not recorded	K6L [(2~{R})-2-[5-(2-hexylphenyl)pentanoylamino]-3-oxidanyl-propyl] dihydrogen phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
7YU8 Human Lysophosphatidic Acid Receptor 1-Gi complex bound to ONO-0740556, state4 Deposited 2022-08-16	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 2–364（363 aa）	Not recorded	K6L [(2~{R})-2-[5-(2-hexylphenyl)pentanoylamino]-3-oxidanyl-propyl] dihydrogen phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.60 Å
9IZF Cryo-EM structure of LPA1-Gi complex with LPA Deposited 2024-08-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 2–364（363 aa）	Not recorded	NKP (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å
9IZG Cryo-EM structure of LPA1-Gq complex with LPA Deposited 2024-08-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 2–364（363 aa）	Not recorded	NKP (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.04 Å
9IZH Cryo-EM structure of LPA1-G13 complex with LPA Deposited 2024-08-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 2–364（363 aa）	Not recorded	NKP (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.04 Å
9J5V Human Lysophosphatidic Acid Receptor 1-Gi complex bound to CpY Deposited 2024-08-13	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 2–364（363 aa）	Not recorded	A1L3Q CpY × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.86 Å

15 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LPAR1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–373； UniProt 2–364

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7yu4
Deposition date deposition_date	2022-08-16
Structure title title	Human Lysophosphatidic Acid Receptor 1-Gi complex bound to ONO-0740556, focused on receptor
Keywords keywords	GPCR, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	20.29 Å
Radius of gyration Rg (electron density) rg_electron	19.18 Å
Forward intensity I(0) i0	12741000.00
Molecular weight molecular_weight	29148.0 kDa
Excluded volume excluded_volume	37502 Å³
Envelope volume envelope_volume	43193 Å³
Hydration-shell volume shell_volume	19032 Å³
Envelope diameter envelope_diameter	65.1 Å
Shell Rg shell_rg	25.45 Å
Envelope Rg envelope_rg	19.64 Å
Shape Rg shape_rg	19.19 Å
Total Rg total_rg	20.18 Å
Total atoms total_atoms	2050
Residues n_residues	266
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

▼

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

Maximum dimension Dmax dmax	65.5 Å
Rg (real space) rg_real	20.30 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	1.2740e+07
I(0) uncertainty (real space) i0_real_error	1.7350e+05
Rg (reciprocal space) rg_reciprocal	20.30 Å
I(0) (reciprocal space) i0_reciprocal	12740000.0000
Solution quality estimate total_estimate	0.8852
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.4 Å
Skewness Skewness skewness	0.375
Kurtosis Kurtosis kurtosis	-0.356
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2524000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.926

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Lysophosphatidic acid receptor 1
Molecular weight formula_weight	42936.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2050

DYKDDDDAMGAAISTSIPVISQPQFTAMNEPQCFYNESIAFFYNRSGKHLATEWNTVSKLVMGLGITVCIFIMLANLLVMVAIYVNRRFHFPIYYLMANLAAADFFAGLAYFYLMFNTGPNTRRLTVSTWLLRQGLIDTSLTASVANLLAIAIERHITVFRMQLHTRMSNRRVVVVIVVIWTMAIVMGAIPSVGWNCICDIENCSNMAPLYSDSYLVFWAIFNLVTFVVMVVLYAHIFGYVRQRTMRMSRHSSGPRRNRDTMMSLLKTVVIVLGAFIICWTPGLVLLLLDVCCPQCDVLAYEKFFLLLAEFNSAMNPIIYSYRDKEMSATFRQILCCQRSENPTGPTEGSDRSASSLNHTILAGVHSNDHSVVENLYFQ

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	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	[(2~{R})-2-[5-(2-hexylphenyl)pentanoylamino]-3-oxidanyl-propyl] dihydrogen phosphate
Molecular weight formula_weight	415.5 kDa
Source method src_method	syn
Copy count entity_count	1

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	7yu4A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily	10 — Rhodopsin 7-helix transmembrane proteins

▶

8. Citations (1)

▶

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	3.700 Å
Low-resolution limit resolution_low	3.700 Å
R factor r_factor	0.4739
R_work r_work	0.4739
R_free r_free	—

Resolution resolution	3.70 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	181071

fit	/app/data/saxs_computation/yu/7yu4/7yu4.fit
pddf	/app/data/pr_computation/yu/7yu4/7yu4.pr.out
profile	/app/data/saxs_computation/yu/7yu4/7yu4.dat

Human Lysophosphatidic Acid Receptor 1-Gi complex bound to ONO-0740556, focused on receptor

1. Protein Identity and Related Structures Protein Identity & Related Structures

Lysophosphatidic acid receptor 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D