8vhf

Cryo-EM structure of GPR119-Gs-Nb35 complex with small molecule agonist MBX-2982

Method: ELECTRON MICROSCOPY Dmax: 118.2 Å Quality: GOOD

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

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

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 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Nanobody35 × 1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092) Soluble cytochrome b562,Glucose-dependent insulinotropic receptor,LgBiT × 1 (P0ABE7,Q8TDV5) 8VP 2-[1-(5-ethylpyrimidin-2-yl)piperidin-4-yl]-4-[[4-(1,2,3,4-tetrazol-1-yl)phenoxy]methyl]-1,3-thiazole × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.51 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 1
Chains and sequence ranges Author chain B; PDBConstruct 7–345; 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 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 1–71 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, HiBiT × 1 (P62873) Nanobody35 × 1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092) Soluble cytochrome b562,Glucose-dependent insulinotropic receptor,LgBiT × 1 (P0ABE7,Q8TDV5) 8VP 2-[1-(5-ethylpyrimidin-2-yl)piperidin-4-yl]-4-[[4-(1,2,3,4-tetrazol-1-yl)phenoxy]methyl]-1,3-thiazole × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.51 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 2
Chains and sequence ranges Author chain C; PDBConstruct 1–71; UniProt 1–71

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 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–394 Mutation:S54N, G226A, E268A, N271K, K274D, R280K, T284D, I285T Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, HiBiT × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Nanobody35 × 1 Soluble cytochrome b562,Glucose-dependent insulinotropic receptor,LgBiT × 1 (P0ABE7,Q8TDV5) 8VP 2-[1-(5-ethylpyrimidin-2-yl)piperidin-4-yl]-4-[[4-(1,2,3,4-tetrazol-1-yl)phenoxy]methyl]-1,3-thiazole × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.51 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 4
Chains and sequence ranges Author chain A; PDBConstruct 1–394; UniProt 1–394

Soluble cytochrome b562,Glucose-dependent insulinotropic receptor,LgBiT

Oplophorus gracilirostris

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 23–128 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, HiBiT × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Nanobody35 × 1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092) 8VP 2-[1-(5-ethylpyrimidin-2-yl)piperidin-4-yl]-4-[[4-(1,2,3,4-tetrazol-1-yl)phenoxy]methyl]-1,3-thiazole × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.51 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 5
Chains and sequence ranges Author chain R; PDBConstruct 3–108; UniProt 23–128

Soluble cytochrome b562,Glucose-dependent insulinotropic receptor,LgBiT

Oplophorus gracilirostris

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 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 1–335 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, HiBiT × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Nanobody35 × 1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092) 8VP 2-[1-(5-ethylpyrimidin-2-yl)piperidin-4-yl]-4-[[4-(1,2,3,4-tetrazol-1-yl)phenoxy]methyl]-1,3-thiazole × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.51 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 113–447; 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 8vhf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8vhf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8vhf
Deposition date deposition_date2024-01-01
Structure title titleCryo-EM structure of GPR119-Gs-Nb35 complex with small molecule agonist MBX-2982
Keywords keywords;CryoEM, GPCR, Orphan, G protein complex, Active, Agonist, MEMBRANE PROTEIN, Diabetes, native Mass Spectrometry, MEMBRANE PROTEIN-SIGNALING PROTEIN complex ;; MEMBRANE PROTEIN/SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier34.05
Radius of gyration Rg (electron density) rg_electron33.89
Forward intensity I(0) i0217481000.00
Molecular weight molecular_weight118130.0 kDa
Excluded volume excluded_volume147790 ų
Envelope volume envelope_volume188960 ų
Hydration-shell volume shell_volume46807 ų
Envelope diameter envelope_diameter125.9
Shell Rg shell_rg40.10
Envelope Rg envelope_rg34.05
Shape Rg shape_rg33.87
Total Rg total_rg34.41
Total atoms total_atoms8299
Residues n_residues1057
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 dmax118.2
Rg (real space) rg_real34.11
Rg uncertainty (real space) rg_real_error0.94
I(0) (real space) i0_real2.1750e+08
I(0) uncertainty (real space) i0_real_error2.8760e+06
Rg (reciprocal space) rg_reciprocal34.07
I(0) (reciprocal space) i0_reciprocal217500000.0000
Solution quality estimate total_estimate0.8643
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.5
Skewness Skewness skewness0.456
Kurtosis Kurtosis kurtosis-0.143
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha56010000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.781; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.901

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)