9vmg

Cryo-EM structure of the spermine-bound sea lamprey TAAR348-Gs complex

Method: ELECTRON MICROSCOPY Dmax: 122.2 Å Quality: EXCELLENT

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

Trace amine-associated receptor 12707.TAAR348

Petromyzon marinus

UniProt A0A678XLR1

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain R; UniProt 1–348 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) Nb35 × 1 scFv16 × 1 SPM SPERMINE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.82 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A678XLR1_PETMA
Isoform
PDB entities 1
Chains and sequence ranges Author chain R; PDBConstruct 1–348; UniProt 1–348

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 1–340 Not recorded Trace amine-associated receptor 12707.TAAR348 × 1 (A0A678XLR1) 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) Nb35 × 1 scFv16 × 1 SPM SPERMINE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.82 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 B; PDBConstruct 1–340; UniProt 1–340

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 1–71 Not recorded Trace amine-associated receptor 12707.TAAR348 × 1 (A0A678XLR1) 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) Nb35 × 1 scFv16 × 1 SPM SPERMINE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.82 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 C; 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 9vmg

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9vmg
Deposition date deposition_date2025-06-27
Structure title titleCryo-EM structure of the spermine-bound sea lamprey TAAR348-Gs complex
Keywords keywordsGPCR, TAAR348, Spermine, Sea lamprey, MEMBRANE PROTEIN/IMMUNE SYSTEM, 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_guinier37.33
Radius of gyration Rg (electron density) rg_electron37.22
Forward intensity I(0) i0301040000.00
Molecular weight molecular_weight139700.0 kDa
Excluded volume excluded_volume174320 ų
Envelope volume envelope_volume221830 ų
Hydration-shell volume shell_volume50517 ų
Envelope diameter envelope_diameter124.4
Shell Rg shell_rg42.33
Envelope Rg envelope_rg37.24
Shape Rg shape_rg37.20
Total Rg total_rg37.59
Total atoms total_atoms9818
Residues n_residues1270
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 dmax122.2
Rg (real space) rg_real37.29
Rg uncertainty (real space) rg_real_error0.84
I(0) (real space) i0_real3.0100e+08
I(0) uncertainty (real space) i0_real_error5.0110e+06
Rg (reciprocal space) rg_reciprocal37.32
I(0) (reciprocal space) i0_reciprocal301000000.0000
Solution quality estimate total_estimate0.9007
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary43.6
Skewness Skewness skewness0.245
Kurtosis Kurtosis kurtosis-0.576
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha54020000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.937

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)