8h2g

Cryo-EM structure of niacin bound human hydroxy-carboxylic acid receptor 2 in complex with Gi heterotrimer

Method: ELECTRON MICROSCOPY Dmax: 126.0 Å Quality: GOOD

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

Hydroxy-carboxylic acid receptor 2

Homo sapiens

UniProt Q8TDS4

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 1–363 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) 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 NIO NICOTINIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;20 mM HEPES pH8.0, 100 mM NaCl, 1 mM MgCl2, 0.5 mM TCEP, 0.001% LMNG, 0.0001% CHS cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.01 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.

39 other PDB entries and 39 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HCAR2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 114–476; UniProt 1–363

Guanine nucleotide-binding protein G(i) subunit alpha-1

Homo sapiens

UniProt P63096

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 1–354 Not recorded Hydroxy-carboxylic acid receptor 2 × 1 (Q8TDS4) 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 NIO NICOTINIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;20 mM HEPES pH8.0, 100 mM NaCl, 1 mM MgCl2, 0.5 mM TCEP, 0.001% LMNG, 0.0001% CHS cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.01 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.

573 other PDB entries and 591 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAI1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–354; UniProt 1–354

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 C; UniProt 2–340 Not recorded Hydroxy-carboxylic acid receptor 2 × 1 (Q8TDS4) Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) scFv16 × 1 NIO NICOTINIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;20 mM HEPES pH8.0, 100 mM NaCl, 1 mM MgCl2, 0.5 mM TCEP, 0.001% LMNG, 0.0001% CHS cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.01 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 3
Chains and sequence ranges Author chain C; 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 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 1–71 Not recorded Hydroxy-carboxylic acid receptor 2 × 1 (Q8TDS4) Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) scFv16 × 1 NIO NICOTINIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;20 mM HEPES pH8.0, 100 mM NaCl, 1 mM MgCl2, 0.5 mM TCEP, 0.001% LMNG, 0.0001% CHS cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.01 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 4
Chains and sequence ranges Author chain D; PDBConstruct 1–71; UniProt 1–71

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 8h2g

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8h2g
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8h2g
Deposition date deposition_date2022-10-06
Structure title titleCryo-EM structure of niacin bound human hydroxy-carboxylic acid receptor 2 in complex with Gi heterotrimer
Keywords keywordsGPCR, Hydroxycarboxylic acid, G-Protein, MEMBRANE PROTEIN, niacin, signaling; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier38.47
Radius of gyration Rg (electron density) rg_electron38.32
Forward intensity I(0) i0246464000.00
Molecular weight molecular_weight128370.0 kDa
Excluded volume excluded_volume161060 ų
Envelope volume envelope_volume214090 ų
Hydration-shell volume shell_volume47754 ų
Envelope diameter envelope_diameter129.3
Shell Rg shell_rg42.56
Envelope Rg envelope_rg38.32
Shape Rg shape_rg38.31
Total Rg total_rg38.62
Total atoms total_atoms9023
Residues n_residues1145
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 dmax126.0
Rg (real space) rg_real38.44
Rg uncertainty (real space) rg_real_error0.81
I(0) (real space) i0_real2.4650e+08
I(0) uncertainty (real space) i0_real_error3.5930e+06
Rg (reciprocal space) rg_reciprocal38.47
I(0) (reciprocal space) i0_reciprocal246500000.0000
Solution quality estimate total_estimate0.8944
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary49.1
Skewness Skewness skewness0.218
Kurtosis Kurtosis kurtosis-0.593
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha37320000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.859

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)