9izg

Cryo-EM structure of LPA1-Gq complex with LPA

Method: ELECTRON MICROSCOPY Dmax: 122.1 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 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 (P63213) Soluble cytochrome b562,Lysophosphatidic acid receptor 1,LgBiT tag × 1 (P0ABE7,Q92633) Gs-mini-Gq chimera × 1 scFv16 × 1 NKP (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.04 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 18–356; UniProt 2–340

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

Mus musculus

UniProt P63213

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 2–71 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Soluble cytochrome b562,Lysophosphatidic acid receptor 1,LgBiT tag × 1 (P0ABE7,Q92633) Gs-mini-Gq chimera × 1 scFv16 × 1 NKP (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.04 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.

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG2_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–70; UniProt 2–71

Soluble cytochrome b562,Lysophosphatidic acid receptor 1,LgBiT tag

synthetic construct

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 23–127 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 (P63213) Gs-mini-Gq chimera × 1 scFv16 × 1 NKP (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.04 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 3
Chains and sequence ranges Author chain R; PDBConstruct 25–129; UniProt 23–127

Soluble cytochrome b562,Lysophosphatidic acid receptor 1,LgBiT tag

synthetic construct

UniProt Q92633

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 2–364 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 (P63213) Gs-mini-Gq chimera × 1 scFv16 × 1 NKP (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.04 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.

15 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LPAR1_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain R; PDBConstruct 131–493; UniProt 2–364

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 9izg

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9izg
Deposition date deposition_date2024-08-01
Structure title titleCryo-EM structure of LPA1-Gq complex with LPA
Keywords keywordsGPCR, SIGNALING PROTEIN, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier38.42
Radius of gyration Rg (electron density) rg_electron38.27
Forward intensity I(0) i0230279000.00
Molecular weight molecular_weight123740.0 kDa
Excluded volume excluded_volume155070 ų
Envelope volume envelope_volume204430 ų
Hydration-shell volume shell_volume45853 ų
Envelope diameter envelope_diameter124.9
Shell Rg shell_rg42.33
Envelope Rg envelope_rg38.09
Shape Rg shape_rg38.25
Total Rg total_rg38.60
Total atoms total_atoms8701
Residues n_residues1149
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 dmax122.1
Rg (real space) rg_real38.37
Rg uncertainty (real space) rg_real_error0.70
I(0) (real space) i0_real2.3030e+08
I(0) uncertainty (real space) i0_real_error3.6490e+06
Rg (reciprocal space) rg_reciprocal38.41
I(0) (reciprocal space) i0_reciprocal230300000.0000
Solution quality estimate total_estimate0.8921
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary50.6
Skewness Skewness skewness0.188
Kurtosis Kurtosis kurtosis-0.658
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha34210000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.745

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)