SAXSdb — 9jqy

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

GFP-like fluorescent chromoprotein,Prostaglandin E2 receptor EP4 subtype

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 2–366	Not recorded	Heavy chain of Fab fragment × 1 Light chain of Fab fragment × 1 A1EC5 ~{N}-[[4-[(5-ethyl-1,3,4-thiadiazol-2-yl)sulfamoyl]phenyl]carbamothioyl]-3-(4-fluorophenyl)propanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.3 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.92 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 9JQY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5YHL Crystal structure of the human prostaglandin E receptor EP4 in complex with Fab and an antagonist Br-derivative Deposited 2017-09-28	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 4–366（363 aa） Fragment：UNP RESIDUES 4-217, 260-366	Mutation：N7Q, A62L, G106R, N177Q, 218-259 deletion	8VL 4-[2-[[(2R)-2-(4-bromanylnaphthalen-1-yl)propanoyl]amino]-4-cyano-phenyl]butanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；24-31% PEG 300, 150 mM potassium sulfate, 100 mM MES (pH 5.5-6.5), 1% 1,2,3-heptanetriol, 0.2 mM ONO-AE3-208-Br, 2% DMSO	Resolution 4.20 Å R-free 0.359
5YWY Crystal structure of the human prostaglandin E receptor EP4 in complex with Fab and ONO-AE3-208 Deposited 2017-11-30	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 4–217（214 aa） Chain A 260–366（107 aa）	Mutation：N7Q, A62L, G106R, N177Q, 218-259 deletion,N7Q, A62L, G106R, N177Q, 218-259 deletion Mutation：N7Q, A62L, G106R, N177Q, 218-259 deletion,N7Q, A62L, G106R, N177Q, 218-259 deletion	7UR 4-[4-cyano-2-[[(2R)-2-(4-fluoranylnaphthalen-1-yl)propanoyl]amino]phenyl]butanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；24-31% PEG 300, 150 mM potassium sulfate, 100 mM MES pH 5.5-6.5, 1% 1,2,3-heptantoriol	Resolution 3.20 Å R-free 0.252
7D7M Cryo-EM Structure of the Prostaglandin E Receptor EP4 Coupled to G Protein Deposited 2020-10-05	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 4–217（214 aa） Chain A 260–366（107 aa）	Mutation：N7Q, N177Q, 218-259 deletion Mutation：N7Q, N177Q, 218-259 deletion	P2E (Z)-7-[(1R,2R,3R)-3-hydroxy-2-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxo-cyclopentyl]hept-5-enoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Blot Force 10, Blot Time 3.5 sec, 3 microL apply	Resolution 3.30 Å
8GCM Cryo-EM Structure of the Prostaglandin E Receptor EP4 Coupled to G Protein Deposited 2023-03-02	Different construct 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 1–488（488 aa）	Not recorded	YX9 (5S)-5-[(3R)-4,4-difluoro-3-hydroxy-4-phenylbutyl]-1-[6-(1H-tetrazol-5-yl)hexyl]pyrrolidin-2-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8GCP Cryo-EM Structure of the Prostaglandin E2 Receptor 4 Coupled to G Protein Deposited 2023-03-02	Different construct 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 1–488（488 aa）	Not recorded	P2E (Z)-7-[(1R,2R,3R)-3-hydroxy-2-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxo-cyclopentyl]hept-5-enoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8GD9 Cryo-EM Structure of the Prostaglandin E2 Receptor 4 Coupled to G Protein Deposited 2023-03-03	Different construct 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 1–488（488 aa）	Not recorded	Z2C 4-({2-[(1R,2R,3R,5S)-3,5-dihydroxy-2-{(3S)-3-hydroxy-4-[3-(methoxymethyl)phenyl]butyl}cyclopentyl]ethyl}sulfanyl)butanoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8GDA Cryo-EM Structure of the Prostaglandin E2 Receptor 4 Coupled to G Protein Deposited 2023-03-03	Different construct 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 1–488（488 aa）	Not recorded	YZV (2S,5R)-5-[(1E,3S)-4,4-difluoro-3-hydroxy-4-phenylbut-1-en-1-yl]-1-[6-(1H-tetrazol-5-yl)hexyl]pyrrolidin-2-ol × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8GDB Cryo-EM Structure of the Prostaglandin E2 Receptor 4 Coupled to G Protein Deposited 2023-03-03	Different construct 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 1–488（488 aa）	Not recorded	P2E (Z)-7-[(1R,2R,3R)-3-hydroxy-2-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxo-cyclopentyl]hept-5-enoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9JQZ Structural Insights into Selective Antagonism Grapiprant and EP4 Prostaglandin Receptor Deposited 2024-09-28	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–366（365 aa）	Mutation：T228A,N232Q,A287L,G331R,N402Q	A1ECR Grapiprant × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.65 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PE2R4_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 227–549； UniProt 2–366

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	9jqy
Deposition date deposition_date	2024-09-28
Structure title title	Structural Insights into Selective Antagonism of TG6-129 and EP4 Prostaglandin Receptor
Keywords keywords	GPCR, MEMBRANE PROTEIN/IMMUNE SYSTEM, MEMBRANE PROTEIN-IMMUNE SYSTEM complex; MEMBRANE PROTEIN/IMMUNE SYSTEM
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	36.80 Å
Radius of gyration Rg (electron density) rg_electron	37.44 Å
Forward intensity I(0) i0	166081000.00
Molecular weight molecular_weight	70486.0 kDa
Excluded volume excluded_volume	68879 Å³
Envelope volume envelope_volume	132030 Å³
Hydration-shell volume shell_volume	33042 Å³
Envelope diameter envelope_diameter	139.6 Å
Shell Rg shell_rg	37.72 Å
Envelope Rg envelope_rg	38.27 Å
Shape Rg shape_rg	37.43 Å
Total Rg total_rg	37.46 Å
Total atoms total_atoms	5338
Residues n_residues	682
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	132.5 Å
Rg (real space) rg_real	37.53 Å
Rg uncertainty (real space) rg_real_error	1.84 Å
I(0) (real space) i0_real	1.6610e+08
I(0) uncertainty (real space) i0_real_error	3.2180e+06
Rg (reciprocal space) rg_reciprocal	37.08 Å
I(0) (reciprocal space) i0_reciprocal	166000000.0000
Solution quality estimate total_estimate	0.7223
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.8 Å
Skewness Skewness skewness	0.703
Kurtosis Kurtosis kurtosis	-0.140
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9082000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.506; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.278; Smooth: 0.593

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Heavy chain of Fab fragment
Molecular weight formula_weight	27574.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	5350

MEWRWIFLFLLSGTTGVHSEIQLQQSGPELVKPGASVKVSCKASGFPFSTYNIYWVIQSHGKSLEWIGYIDPYNGGTSYNQKFRGKATLTVDKSSSTAYMHLNSLTSEDSAVYYCARRWYTYDGDWFAYWGQGTLVTVSAAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPTIKPCPPCKCP

来源 Source

来源生物 organism	Mus musculus
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Light chain of Fab fragment
Molecular weight formula_weight	28944.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MDMRTPAQFLGILLLWFPGIKCDIKMTQSPSSMYVSLGERVTITCKASQDINRYLSWFQQKPGKSPKTLIYRANRMLDGVPSRFSGSGSGQDYSLTISSLEYEDMGNYYCLQYDEFPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNECVDENLYFQGASHHHHHHHH

来源 Source

来源生物 organism	Mus musculus
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	GFP-like fluorescent chromoprotein,Prostaglandin E2 receptor EP4 subtype
Molecular weight formula_weight	61463.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

ASVIKPEMKIKLRMEGAVNGHKFVIEGEGIGKPYEGTQTLDLTVEEGAPLPFSYDILTPAFQYGNRAFTKYPEDIPDYFKQAFPEGYSWERSMTYEDQGICIATSDITMEGDCFFYEIRFDGTNFPPNGPVMQKKTLKWEPSTEKMYVEDGVLKGDVEMALLLEGGGHYRCDFKTTYKAKKDVRLPDAHEVDHRIEILSHDKDYNKVRLYEHAEARYSGGGSGGGGSAPGVQSSASLSPDRLNSPVTIPAVMFIFGVVGNLVAIVVLCKSRKEQKETTFYTLVCGLLVTDLLGTLLVSPVTIATYMKGQWPGGQPLCEYSTFILLFFSLSRLSIICAMSVERYLAINHAYFYSHYVDKRLAGLTLFAVYASNVLFCALPNMGLGSSRLQYPDTWCFIDWTTQVTAHAAYSYMYAGFSSFLILATVLCNVLVCGALLRMHRQFFRRIAGAEIQMVILLIATSLVVLICSIPLVVRVFVNQLYQPSLEREVSKNPDLQAIRIASVNPILDPWIYILLRKTVLSKAIEKIKCLFCRIGGSRRERSGQHCSDS

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 4 Entity 4 non-polymer

Description description	~{N}-[[4-[(5-ethyl-1,3,4-thiadiazol-2-yl)sulfamoyl]phenyl]carbamothioyl]-3-(4-fluorophenyl)propanamide
Molecular weight formula_weight	493.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	6

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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	2.92 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	97395

fit	/app/data/saxs_computation/jq/9jqy/9jqy.fit
pddf	/app/data/pr_computation/jq/9jqy/9jqy.pr.out
profile	/app/data/saxs_computation/jq/9jqy/9jqy.dat

Structural Insights into Selective Antagonism of TG6-129 and EP4 Prostaglandin Receptor

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

GFP-like fluorescent chromoprotein,Prostaglandin E2 receptor EP4 subtype

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)