9xjw

Cryo-EM structure of GPR119 in complex with partial agonist AS1268574 and Gs protein

Method: ELECTRON MICROSCOPY Dmax: 115.4 Å Quality: REASONABLE

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

Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

Homo sapiens

UniProt P63092

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–394 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Nb35 × 1 Glucose-dependent insulinotropic receptor × 1 (Q8TDV5) A1E0J 2-[[2-(4-bromophenyl)-6-methyl-pyrimidin-4-yl]amino]ethanol × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.53 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.

348 other PDB entries and 356 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAS2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–394; UniProt 1–394

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Homo sapiens

UniProt P62873

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Nb35 × 1 Glucose-dependent insulinotropic receptor × 1 (Q8TDV5) A1E0J 2-[[2-(4-bromophenyl)-6-methyl-pyrimidin-4-yl]amino]ethanol × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.53 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.

1260 other PDB entries and 1263 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 13–351; UniProt 2–340

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

Homo sapiens

UniProt P59768

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 1–71 Not recorded Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Nb35 × 1 Glucose-dependent insulinotropic receptor × 1 (Q8TDV5) A1E0J 2-[[2-(4-bromophenyl)-6-methyl-pyrimidin-4-yl]amino]ethanol × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.53 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.

1233 other PDB entries and 1236 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG2_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–71; UniProt 1–71

Glucose-dependent insulinotropic receptor

Homo sapiens

UniProt Q8TDV5

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 1–335 Not recorded Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Nb35 × 1 A1E0J 2-[[2-(4-bromophenyl)-6-methyl-pyrimidin-4-yl]amino]ethanol × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.53 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.

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

View Construct and Data Evidence
UniProt name GP119_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain R; PDBConstruct 1–335; UniProt 1–335

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 9xjw

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9xjw
Deposition date deposition_date2025-11-05
Structure title titleCryo-EM structure of GPR119 in complex with partial agonist AS1268574 and Gs protein
Keywords keywordsGPCR, Complex, Signal transduction, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier34.75
Radius of gyration Rg (electron density) rg_electron34.61
Forward intensity I(0) i0409989000.00
Molecular weight molecular_weight108330.0 kDa
Excluded volume excluded_volume104360 ų
Envelope volume envelope_volume191460 ų
Hydration-shell volume shell_volume46785 ų
Envelope diameter envelope_diameter123.5
Shell Rg shell_rg40.39
Envelope Rg envelope_rg34.67
Shape Rg shape_rg34.60
Total Rg total_rg34.91
Total atoms total_atoms8182
Residues n_residues1047
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 dmax115.4
Rg (real space) rg_real34.82
Rg uncertainty (real space) rg_real_error0.90
I(0) (real space) i0_real4.1000e+08
I(0) uncertainty (real space) i0_real_error6.7580e+06
Rg (reciprocal space) rg_reciprocal34.78
I(0) (reciprocal space) i0_reciprocal410000000.0000
Solution quality estimate total_estimate0.6500
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.6
Skewness Skewness skewness0.436
Kurtosis Kurtosis kurtosis-0.201
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha56210000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 0.038; Positv: 1.000; Valcen: 0.995; Smooth: 0.745

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)