8jbf

Senktide bound to active human neurokinin 3 receptor in complex with Gq

Method: ELECTRON MICROSCOPY Dmax: 119.6 Å Quality: GOOD

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

Neuromedin-K receptor

Homo sapiens

UniProt P29371

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 1–394 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) ScFv16 nanobody × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Senktide × 1 Guanine nucleotide-binding protein Gq subunit alpha × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 3.00 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 NK3R_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain B; PDBConstruct 1–394; UniProt 1–394

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Rattus norvegicus

UniProt P54311

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 D; UniProt 2–340 Not recorded Neuromedin-K receptor × 1 (P29371) ScFv16 nanobody × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Senktide × 1 Guanine nucleotide-binding protein Gq subunit alpha × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 3.00 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.

161 other PDB entries and 162 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_RAT
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 13–351; UniProt 2–340

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

Bos taurus

UniProt P63212

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 G; UniProt 1–71 Not recorded Neuromedin-K receptor × 1 (P29371) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) ScFv16 nanobody × 1 Senktide × 1 Guanine nucleotide-binding protein Gq subunit alpha × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 3.00 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.

215 other PDB entries and 216 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG2_BOVIN
Isoform
PDB entities 4
Chains and sequence ranges Author chain G; 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 8jbf

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8jbf
Deposition date deposition_date2023-05-08
Structure title titleSenktide bound to active human neurokinin 3 receptor in complex with Gq
Keywords keywordsG protein coupled receptor, Neurokinin, Cryo-EM, Peptide Agonists, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier37.98
Radius of gyration Rg (electron density) rg_electron37.87
Forward intensity I(0) i0232582000.00
Molecular weight molecular_weight124860.0 kDa
Excluded volume excluded_volume156640 ų
Envelope volume envelope_volume203750 ų
Hydration-shell volume shell_volume45982 ų
Envelope diameter envelope_diameter124.3
Shell Rg shell_rg42.15
Envelope Rg envelope_rg37.83
Shape Rg shape_rg37.87
Total Rg total_rg38.12
Total atoms total_atoms8783
Residues n_residues1144
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 dmax119.6
Rg (real space) rg_real37.93
Rg uncertainty (real space) rg_real_error0.83
I(0) (real space) i0_real2.3260e+08
I(0) uncertainty (real space) i0_real_error4.0320e+06
Rg (reciprocal space) rg_reciprocal37.97
I(0) (reciprocal space) i0_reciprocal232600000.0000
Solution quality estimate total_estimate0.8895
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary48.4
Skewness Skewness skewness0.190
Kurtosis Kurtosis kurtosis-0.652
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha34020000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.686

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)