8k6o

Structural complex of neuropeptide Y receptor 1

Method: ELECTRON MICROSCOPY Dmax: 134.3 Å Quality: REASONABLE

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

Guanine nucleotide-binding protein G(i) subunit alpha-2

Homo sapiens

UniProt P04899

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 A; UniProt 1–355 Mutation:S47N,G204A,E246A,A327S 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) Neuropeptide Y receptor type 1 × 1 (P25929) scFV16 × 1 C-flanking peptide of NPY × 1 (P01303) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.30 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.

30 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAI2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–355; UniProt 1–355

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 Protein heterocomplex 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) subunit alpha-2 × 1 (P04899) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Neuropeptide Y receptor type 1 × 1 (P25929) scFV16 × 1 C-flanking peptide of NPY × 1 (P01303) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.30 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 2
Chains and sequence ranges Author chain B; PDBConstruct 18–356; 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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 1–71 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-2 × 1 (P04899) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Neuropeptide Y receptor type 1 × 1 (P25929) scFV16 × 1 C-flanking peptide of NPY × 1 (P01303) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.30 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 3
Chains and sequence ranges Author chain C; PDBConstruct 1–71; UniProt 1–71

Neuropeptide Y receptor type 1

Homo sapiens

UniProt P25929

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 1–341 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-2 × 1 (P04899) 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 C-flanking peptide of NPY × 1 (P01303) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.30 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 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NPY1R_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–341; UniProt 1–341

C-flanking peptide of NPY

OrganismNot specified

UniProt P01303

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 E; UniProt 29–64 Mutation:I31L,Q34P Guanine nucleotide-binding protein G(i) subunit alpha-2 × 1 (P04899) 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) Neuropeptide Y receptor type 1 × 1 (P25929) scFV16 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.30 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.

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NPY_HUMAN
Isoform
PDB entities 6
Chains and sequence ranges Author chain E; PDBConstruct 1–36; UniProt 29–64

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 8k6o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8k6o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8k6o
Deposition date deposition_date2023-07-25
Structure title titleStructural complex of neuropeptide Y receptor 1
Keywords keywordsneuropeptide Y receptor 1, complex, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier40.42
Radius of gyration Rg (electron density) rg_electron40.30
Forward intensity I(0) i0263854000.00
Molecular weight molecular_weight132870.0 kDa
Excluded volume excluded_volume166650 ų
Envelope volume envelope_volume230540 ų
Hydration-shell volume shell_volume49287 ų
Envelope diameter envelope_diameter143.9
Shell Rg shell_rg43.78
Envelope Rg envelope_rg40.15
Shape Rg shape_rg40.30
Total Rg total_rg40.51
Total atoms total_atoms9333
Residues n_residues1183
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 dmax134.3
Rg (real space) rg_real40.43
Rg uncertainty (real space) rg_real_error1.16
I(0) (real space) i0_real2.6390e+08
I(0) uncertainty (real space) i0_real_error4.9070e+06
Rg (reciprocal space) rg_reciprocal40.42
I(0) (reciprocal space) i0_reciprocal263900000.0000
Solution quality estimate total_estimate0.6817
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary51.6
Skewness Skewness skewness0.262
Kurtosis Kurtosis kurtosis-0.516
Angular range angular_range— – 0.1950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha43410000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 0.107; Positv: 1.000; Valcen: 0.944; Smooth: 0.869

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)