SAXSdb — 5yhl

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

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 4–366	Fragment：UNP RESIDUES 4-217, 260-366 Mutation：N7Q, A62L, G106R, N177Q, 218-259 deletion	Heavy chain of Fab fragment × 1 Light chain of Fab fragment × 1 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

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 5YHL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 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 method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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
9JQY Structural Insights into Selective Antagonism of TG6-129 and EP4 Prostaglandin Receptor Deposited 2024-09-28	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 2–366（365 aa）	Not recorded	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
9JQZ Structural Insights into Selective Antagonism Grapiprant and EP4 Prostaglandin Receptor Deposited 2024-09-28	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 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–324； UniProt 4–366

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	5yhl
Deposition date deposition_date	2017-09-28
Structure title title	Crystal structure of the human prostaglandin E receptor EP4 in complex with Fab and an antagonist Br-derivative
Keywords keywords	G-protein coupled receptor, lipid mediator, functional antibody, SIGNALING PROTEIN-IMMUNE SYSTEM complex; SIGNALING PROTEIN/IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	36.94 Å
Radius of gyration Rg (electron density) rg_electron	37.69 Å
Forward intensity I(0) i0	93403300.00
Molecular weight molecular_weight	79727.0 kDa
Excluded volume excluded_volume	100630 Å³
Envelope volume envelope_volume	135350 Å³
Hydration-shell volume shell_volume	33628 Å³
Envelope diameter envelope_diameter	135.3 Å
Shell Rg shell_rg	38.29 Å
Envelope Rg envelope_rg	38.31 Å
Shape Rg shape_rg	37.61 Å
Total Rg total_rg	38.01 Å
Total atoms total_atoms	5607
Residues n_residues	717
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	128.8 Å
Rg (real space) rg_real	37.65 Å
Rg uncertainty (real space) rg_real_error	1.40 Å
I(0) (real space) i0_real	9.3400e+07
I(0) uncertainty (real space) i0_real_error	1.7180e+06
Rg (reciprocal space) rg_reciprocal	37.21 Å
I(0) (reciprocal space) i0_reciprocal	93360000.0000
Solution quality estimate total_estimate	0.7327
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.0 Å
Skewness Skewness skewness	0.703
Kurtosis Kurtosis kurtosis	-0.107
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11540000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.606; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.376; Smooth: 0.330

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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	Prostaglandin E2 receptor EP4 subtype
Molecular weight formula_weight	37063.5 kDa
Mutation mutation	N7Q, A62L, G106R, N177Q, 218-259 deletion
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	5613

GTSPGVQSSASLSPDRLNSPVTIPAVMFIFGVVGNLVAIVVLCKSRKEQKETTFYTLVCGLLVTDLLGTLLVSPVTIATYMKGQWPGGQPLCEYSTFILLFFSLSRLSIICAMSVERYLAINHAYFYSHYVDKRLAGLTLFAVYASNVLFCALPNMGLGSSRLQYPDTWCFIDWTTQVTAHAAYSYMYAGFSSFLILATVLCNVLVCGALLRMHRQFFRRIAGAEIQMVILLIATSLVVLICSIPLVVRVFVNQLYQPSLEREVSKNPDLQAIRIASVNPILDPWIYILLRKTVLSKAIEKIKCLFCRIGGSRRERSGQHCSDSLEENLYFQ

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 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

MEWRWIFLFLLSGTTGVHSEIQLQQSGPELVKPGASVKVSCKASGFPFSTYNIYWVIQSHGKSLEWIGYIDPYNGGTSYNQKFRGKATLTVDKSSSTAYMHLNSLTSEDSAVYYCARRWYTYDGDWFAYWGQGTLVTVSAAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPTIKPCPPCKCP

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	hybrid

Entity 3 Entity 3 polymer

Description description	Light chain of Fab fragment
Molecular weight formula_weight	26614.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MDMRTPAQFLGILLLWFPGIKCDIKMTQSPSSMYVSLGERVTITCKASQDINRYLSWFQQKPGKSPKTLIYRANRMLDGVPSRFSGSGSGQDYSLTISSLEYEDMGNYYCLQYDEFPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	hybrid

Entity 4 Entity 4 non-polymer

Description description	4-[2-[[(2R)-2-(4-bromanylnaphthalen-1-yl)propanoyl]amino]-4-cyano-phenyl]butanoic acid
Molecular weight formula_weight	465.3 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	101.970 Å
Unit-cell length b length_b	392.230 Å
Unit-cell length c length_c	81.080 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	4.200 Å
Low-resolution limit resolution_low	49.339 Å
R factor r_factor	0.3343
R_work r_work	0.3330
R_free r_free	0.3588

fit	/app/data/saxs_computation/yh/5yhl/5yhl.fit
pddf	/app/data/pr_computation/yh/5yhl/5yhl.pr.out
profile	/app/data/saxs_computation/yh/5yhl/5yhl.dat

Crystal structure of the human prostaglandin E receptor EP4 in complex with Fab and an antagonist Br-derivative

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

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)