8z3y

Cryo-EM structure of of hGPR4-Gs complex in pH6.8

Method: ELECTRON MICROSCOPY Dmax: 123.5 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

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 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) scFv16 × 1 G-protein coupled receptor 4 × 1 (P46093) ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.20 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 G; UniProt 5–63 Not recorded Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) scFv16 × 1 G-protein coupled receptor 4 × 1 (P46093) ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.20 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 G; PDBConstruct 1–59; UniProt 5–63

G-protein coupled receptor 4

Homo sapiens

UniProt P46093

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 1–362 Not recorded Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 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) scFv16 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.20 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.

24 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GPR4_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain R; PDBConstruct 1–362; UniProt 1–362

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 8z3y

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8z3y
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8z3y
Deposition date deposition_date2024-04-16
Structure title titleCryo-EM structure of of hGPR4-Gs complex in pH6.8
Keywords keywordspH6.8, hGPR4, MEMBRANE PROTEIN, MEMBRANE PROTEIN-IMMUNE SYSTEM complex; MEMBRANE PROTEIN/IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier38.29
Radius of gyration Rg (electron density) rg_electron38.16
Forward intensity I(0) i0222308000.00
Molecular weight molecular_weight121320.0 kDa
Excluded volume excluded_volume151880 ų
Envelope volume envelope_volume208020 ų
Hydration-shell volume shell_volume46650 ų
Envelope diameter envelope_diameter128.4
Shell Rg shell_rg42.44
Envelope Rg envelope_rg38.04
Shape Rg shape_rg38.21
Total Rg total_rg38.27
Total atoms total_atoms8557
Residues n_residues1151
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 dmax123.5
Rg (real space) rg_real38.25
Rg uncertainty (real space) rg_real_error0.89
I(0) (real space) i0_real2.2230e+08
I(0) uncertainty (real space) i0_real_error3.6440e+06
Rg (reciprocal space) rg_reciprocal38.28
I(0) (reciprocal space) i0_reciprocal222300000.0000
Solution quality estimate total_estimate0.8974
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary48.2
Skewness Skewness skewness0.201
Kurtosis Kurtosis kurtosis-0.630
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha37280000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.851

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)