9u4y

cryo-EM structure of Xenopus laevis GnRHR bound with mammal GnRH

Method: ELECTRON MICROSCOPY Dmax: 124.7 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 × 6 PDB declaration: hexameric(6) 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) Gonadoliberin-1 × 1 (Q28588) Guanine nucleotide-binding protein G(q) subunit alpha-1 × 1 scFv16 × 1 Beta-2 adrenergic receptor,Gonadotropin-releasing hormone receptor × 1 (P07550,Q90WJ2) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.67 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 6–344; 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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain G; UniProt 1–71 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Gonadoliberin-1 × 1 (Q28588) Guanine nucleotide-binding protein G(q) subunit alpha-1 × 1 scFv16 × 1 Beta-2 adrenergic receptor,Gonadotropin-releasing hormone receptor × 1 (P07550,Q90WJ2) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.67 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 G; PDBConstruct 1–71; UniProt 1–71

Gonadoliberin-1

OrganismNot specified

UniProt Q28588

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 1–10 Non-standard monomer:Yes (specific site not provided by mmCIF) 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) Guanine nucleotide-binding protein G(q) subunit alpha-1 × 1 scFv16 × 1 Beta-2 adrenergic receptor,Gonadotropin-releasing hormone receptor × 1 (P07550,Q90WJ2) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.67 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 GON1_SHEEP
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–10; UniProt 1–10

Beta-2 adrenergic receptor,Gonadotropin-releasing hormone receptor

Xenopus laevis

UniProt P07550

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain R; UniProt 1–30 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 (P59768) Gonadoliberin-1 × 1 (Q28588) Guanine nucleotide-binding protein G(q) subunit alpha-1 × 1 scFv16 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.67 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.

143 other PDB entries and 145 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ADRB2_HUMAN
Isoform
PDB entities 6
Chains and sequence ranges Author chain R; PDBConstruct 48–77; UniProt 1–30

Beta-2 adrenergic receptor,Gonadotropin-releasing hormone receptor

Xenopus laevis

UniProt Q90WJ2

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain R; UniProt 1–418 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 (P59768) Gonadoliberin-1 × 1 (Q28588) Guanine nucleotide-binding protein G(q) subunit alpha-1 × 1 scFv16 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.67 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 Q90WJ2_XENLA
Isoform
PDB entities 6
Chains and sequence ranges Author chain R; PDBConstruct 87–504; UniProt 1–418

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 9u4y

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9u4y
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9u4y
Deposition date deposition_date2025-03-20
Structure title titlecryo-EM structure of Xenopus laevis GnRHR bound with mammal GnRH
Keywords keywordsCryo-EM, GnRHR, Gonadotropin-Releasing Hormone Receptor, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier38.08
Radius of gyration Rg (electron density) rg_electron38.00
Forward intensity I(0) i0232512000.00
Molecular weight molecular_weight124640.0 kDa
Excluded volume excluded_volume156440 ų
Envelope volume envelope_volume206230 ų
Hydration-shell volume shell_volume46632 ų
Envelope diameter envelope_diameter126.9
Shell Rg shell_rg42.16
Envelope Rg envelope_rg37.80
Shape Rg shape_rg38.01
Total Rg total_rg38.23
Total atoms total_atoms17343
Residues n_residues1117
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 dmax124.7
Rg (real space) rg_real38.04
Rg uncertainty (real space) rg_real_error1.15
I(0) (real space) i0_real2.3250e+08
I(0) uncertainty (real space) i0_real_error4.0760e+06
Rg (reciprocal space) rg_reciprocal38.07
I(0) (reciprocal space) i0_reciprocal232500000.0000
Solution quality estimate total_estimate0.8991
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.5
Skewness Skewness skewness0.199
Kurtosis Kurtosis kurtosis-0.643
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha36810000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.931

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)