SAXSdb — 8iyx

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

Probable G-protein coupled receptor 34,Probable G-protein coupled receptor 34,YL-365

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 C； UniProt 1–251 Chain C； UniProt 259–381	Not recorded	S6R 1-[4-(3-chlorophenyl)phenyl]carbonyl-4-[2-(4-phenylmethoxyphenyl)ethanoylamino]piperidine-4-carboxylic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.34 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 8IYX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8IZ4 Lysophosphatidylserine receptor GPR34-Gi complex Deposited 2023-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–344（344 aa）	Not recorded	TJR [(2~{R})-2-oxidanyl-3-phosphonooxy-propyl] octadecanoate × 1 SER SERINE × 1 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.93 Å
8K4N Structure of GPR34-Gi complex Deposited 2023-07-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: hexameric	Chain D 49–327（279 aa）	Not recorded	VF0 (2R)-2-azanyl-3-[oxidanyl-[(2R)-2-oxidanyl-3-tetradec-9-enoyloxy-propoxy]phosphoryl]oxy-propanoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.83 Å
8SAI Cryo-EM structure of GPR34-Gi complex Deposited 2023-04-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 38–373（336 aa）	Not recorded	S12 O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.27 Å
8WRB Lysophosphatidylserine receptor GPR34-Gi complex Deposited 2023-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–344（344 aa）	Not recorded	CLR CHOLESTEROL × 1 SER SERINE × 1 UBL [(2R)-2-oxidanyl-3-phosphonooxy-propyl] (Z)-octadec-9-enoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.91 Å
8XBE Human GPR34 -Gi complex bound to S3E-LysoPS Deposited 2023-12-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 2–381（380 aa）	Not recorded	KW0 (2~{S})-2-azanyl-3-[[(2~{R})-1-ethoxy-3-[(~{Z})-octadec-9-enoyl]oxy-propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8XBG Human GPR34 -Gi complex bound to S3E-LysoPS, receptor focused Deposited 2023-12-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–381（380 aa）	Not recorded	KW0 (2~{S})-2-azanyl-3-[[(2~{R})-1-ethoxy-3-[(~{Z})-octadec-9-enoyl]oxy-propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.43 Å
8XBH Human GPR34 -Gi complex bound to M1 Deposited 2023-12-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 2–381（380 aa）	Not recorded	KW3 (2~{S})-2-azanyl-3-[[(2~{R})-1-ethoxy-3-[3-[2-[(3-phenoxyphenyl)methoxy]phenyl]propanoyloxy]propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.83 Å
8XBI Human GPR34 -Gi complex bound to M1, receptor focused Deposited 2023-12-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain R 2–381（380 aa）	Not recorded	KW3 (2~{S})-2-azanyl-3-[[(2~{R})-1-ethoxy-3-[3-[2-[(3-phenoxyphenyl)methoxy]phenyl]propanoyloxy]propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.06 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GPR34_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–251； UniProt 1–251 Author chain C； PDBConstruct 459–581； UniProt 259–381

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8iyx
Deposition date deposition_date	2023-04-06
Structure title title	Cryo-EM structure of the GPR34 receptor in complex with the antagonist YL-365
Keywords keywords	Inhibitor, GPR34 receptor in complex with the antagonist YL-365, MEMBRANE PROTEIN, MEMBRANE PROTEIN-INHIBITOR complex; MEMBRANE PROTEIN/INHIBITOR
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	21.06 Å
Radius of gyration Rg (electron density) rg_electron	20.01 Å
Forward intensity I(0) i0	13441100.00
Molecular weight molecular_weight	31367.0 kDa
Excluded volume excluded_volume	40982 Å³
Envelope volume envelope_volume	48843 Å³
Hydration-shell volume shell_volume	20605 Å³
Envelope diameter envelope_diameter	69.0 Å
Shell Rg shell_rg	26.25 Å
Envelope Rg envelope_rg	20.30 Å
Shape Rg shape_rg	19.97 Å
Total Rg total_rg	21.15 Å
Total atoms total_atoms	2207
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

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

Maximum dimension Dmax dmax	67.3 Å
Rg (real space) rg_real	21.04 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	1.3440e+07
I(0) uncertainty (real space) i0_real_error	1.7750e+05
Rg (reciprocal space) rg_reciprocal	21.05 Å
I(0) (reciprocal space) i0_reciprocal	13440000.0000
Solution quality estimate total_estimate	0.8933
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.8 Å
Skewness Skewness skewness	0.327
Kurtosis Kurtosis kurtosis	-0.399
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2501000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.972

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Probable G-protein coupled receptor 34,Probable G-protein coupled receptor 34,YL-365
Molecular weight formula_weight	66231.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	2207

MRSHTITMTTTSVSSWPYSSHRMRFITNHSDQPPQNFSATPNVTTCPMDEKLLSTVLTTSYSVIFIVGLVGNIIALYVFLGIHRKRNSIQIYLLNVAIADLLLIFCLPFRIMYHINQNKWTLGVILCKVVGTLFYMNMYISIILLGFISLDRYIKINRSIQQRKAITTKQSIYVCCIVWMLALGGFLTMIILTLKKGGHNSTMCFHYRDKHNAKGEAIFNFILVVMFWLIFLLIILSYIKIGKNLLRISKRGIDCSFWNESYLTGSRDERKKSLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSDQARMDIRLAKGKYATTARNSFIVLIIFTICFVPYHAFRFIYISSQLNVSSCYWKEIVHKTNEIMLVLSSFNSCLDPVMYFLMSSNIRKIMCQLLFRRFQGEPSRSESTSEFKPGYSLHDTSVAVKIQSSSKST

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	1-[4-(3-chlorophenyl)phenyl]carbonyl-4-[2-(4-phenylmethoxyphenyl)ethanoylamino]piperidine-4-carboxylic acid
Molecular weight formula_weight	583.1 kDa
Source method src_method	syn
Copy count entity_count	1

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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	3.34 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	3266074

fit	/app/data/saxs_computation/iy/8iyx/8iyx.fit
pddf	/app/data/pr_computation/iy/8iyx/8iyx.pr.out
profile	/app/data/saxs_computation/iy/8iyx/8iyx.dat

Cryo-EM structure of the GPR34 receptor in complex with the antagonist YL-365

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

Probable G-protein coupled receptor 34,Probable G-protein coupled receptor 34,YL-365

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)