8zjd

Cryo-EM structure of kisspeptin receptor bound to KP-10

Method: ELECTRON MICROSCOPY Dmax: 122.6 Å Quality: EXCELLENT

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

KiSS-1 receptor,KiSS-1 receptor,KiSS-1 receptor,KiSS-1 receptor,KiSS-1 receptor, G-protein coupled receptor 54, GPR54, KISS1R

Homo sapiens

UniProt Q969F8

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 2–355 Not recorded kisspeptin-10 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) scFv16 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha × 1 (P63096,P50148) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.06 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.

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KISSR_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain R; PDBConstruct 1–354; UniProt 2–355

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 KiSS-1 receptor,KiSS-1 receptor,KiSS-1 receptor,KiSS-1 receptor,KiSS-1 receptor, G-protein coupled receptor 54, GPR54, KISS1R × 1 (Q969F8) kisspeptin-10 × 1 scFv16 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha × 1 (P63096,P50148) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.06 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 13–351; 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 KiSS-1 receptor,KiSS-1 receptor,KiSS-1 receptor,KiSS-1 receptor,KiSS-1 receptor, G-protein coupled receptor 54, GPR54, KISS1R × 1 (Q969F8) kisspeptin-10 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) scFv16 × 1 Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha × 1 (P63096,P50148) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.06 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 5
Chains and sequence ranges Author chain G; PDBConstruct 1–71; UniProt 1–71

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

Homo sapiens

UniProt P50148

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 A; UniProt 37–359 Not recorded KiSS-1 receptor,KiSS-1 receptor,KiSS-1 receptor,KiSS-1 receptor,KiSS-1 receptor, G-protein coupled receptor 54, GPR54, KISS1R × 1 (Q969F8) kisspeptin-10 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) scFv16 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.06 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.

33 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAQ_HUMAN
Isoform
PDB entities 6
Chains and sequence ranges Author chain A; PDBConstruct 31–353; UniProt 37–359

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

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 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–28 Not recorded KiSS-1 receptor,KiSS-1 receptor,KiSS-1 receptor,KiSS-1 receptor,KiSS-1 receptor, G-protein coupled receptor 54, GPR54, KISS1R × 1 (Q969F8) kisspeptin-10 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) scFv16 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.06 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 6
Chains and sequence ranges Author chain A; PDBConstruct 1–28; UniProt 1–28

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 8zjd

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8zjd
Deposition date deposition_date2024-05-14
Structure title titleCryo-EM structure of kisspeptin receptor bound to KP-10
Keywords keywordsCryo-EM, kisspeptin receptor, GPR54, KISS1R, G proteins, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier37.72
Radius of gyration Rg (electron density) rg_electron37.60
Forward intensity I(0) i0237140000.00
Molecular weight molecular_weight125330.0 kDa
Excluded volume excluded_volume157030 ų
Envelope volume envelope_volume206740 ų
Hydration-shell volume shell_volume47123 ų
Envelope diameter envelope_diameter126.2
Shell Rg shell_rg42.25
Envelope Rg envelope_rg37.40
Shape Rg shape_rg37.61
Total Rg total_rg37.84
Total atoms total_atoms8820
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 dmax122.6
Rg (real space) rg_real37.65
Rg uncertainty (real space) rg_real_error0.96
I(0) (real space) i0_real2.3710e+08
I(0) uncertainty (real space) i0_real_error3.8830e+06
Rg (reciprocal space) rg_reciprocal37.70
I(0) (reciprocal space) i0_reciprocal237200000.0000
Solution quality estimate total_estimate0.9029
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary49.6
Skewness Skewness skewness0.178
Kurtosis Kurtosis kurtosis-0.647
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha37680000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.940

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)