9ekh

Cryo-EM structure ONO3030297-bound prostaglandin D2 receptor (DP1)-bRIL-Fab complex

Method: ELECTRON MICROSCOPY Dmax: 159.6 Å Quality: GOOD

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

Prostaglandin D2 receptor,Soluble cytochrome b562

Homo sapiens

UniProt P0ABE7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 23–128 Not recorded anti-BRIL Fab Heavy Chain × 1 anti-Fab Nanobody × 1 anti-BRIL Fab Light Chain × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 A1BI8 1-[2-chloro-5-(2,6-dimethyl-4-{[(2S)-4-methyl-3,4-dihydro-2H-1,4-benzoxazin-2-yl]methoxy}benzamido)phenyl]cyclopropane-1-carboxylic acid × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.89 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.

714 other PDB entries and 822 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C562_ECOLX
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 260–365; UniProt 23–128

Prostaglandin D2 receptor,Soluble cytochrome b562

Homo sapiens

UniProt Q13258

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–233 Chain A; UniProt 258–359 Not recorded anti-BRIL Fab Heavy Chain × 1 anti-Fab Nanobody × 1 anti-BRIL Fab Light Chain × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 A1BI8 1-[2-chloro-5-(2,6-dimethyl-4-{[(2S)-4-methyl-3,4-dihydro-2H-1,4-benzoxazin-2-yl]methoxy}benzamido)phenyl]cyclopropane-1-carboxylic acid × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.89 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.

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PD2R_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 27–259; UniProt 1–233 Author chain A; PDBConstruct 373–474; UniProt 258–359

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

SAXS profile for 9ekh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9ekh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9ekh
Deposition date deposition_date2024-12-02
Structure title titleCryo-EM structure ONO3030297-bound prostaglandin D2 receptor (DP1)-bRIL-Fab complex
Keywords keywords;GPCR, cryo-EM, DP1, inverse agonist, ONO3030297, prostaglandin D2 receptor, prostanoid DP receptor, PGD receptor, PTGDR, DP1-bRIL chimera, MEMBRANE PROTEIN ;; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier45.21
Radius of gyration Rg (electron density) rg_electron45.60
Forward intensity I(0) i0329801000.00
Molecular weight molecular_weight99602.0 kDa
Excluded volume excluded_volume96596 ų
Envelope volume envelope_volume206570 ų
Hydration-shell volume shell_volume39711 ų
Envelope diameter envelope_diameter154.1
Shell Rg shell_rg47.11
Envelope Rg envelope_rg44.29
Shape Rg shape_rg45.57
Total Rg total_rg45.71
Total atoms total_atoms7546
Residues n_residues974
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax159.6
Rg (real space) rg_real45.63
Rg uncertainty (real space) rg_real_error2.60
I(0) (real space) i0_real3.2980e+08
I(0) uncertainty (real space) i0_real_error7.2080e+06
Rg (reciprocal space) rg_reciprocal45.21
I(0) (reciprocal space) i0_reciprocal329600000.0000
Solution quality estimate total_estimate0.8032
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.9
Skewness Skewness skewness0.401
Kurtosis Kurtosis kurtosis-0.622
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9456000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.719; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.491; Smooth: 0.790

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)