9m1o

Cryo-EM structures of NPFFR2 complex with neuropeptide FF

Method: ELECTRON MICROSCOPY Dmax: 129.6 Å Quality: GOOD

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

Soluble cytochrome b562,Neuropeptide FF receptor 2,Neuropeptide FF receptor 2

Homo sapiens

UniProt Q9Y5X5

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 103–522 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Morphine-modulating neuropeptide B × 1 (P15507) scfv16 × 1 Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.49 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.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NPFF2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain R; PDBConstruct 158–577; UniProt 103–522

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 B; UniProt 2–340 Not recorded Soluble cytochrome b562,Neuropeptide FF receptor 2,Neuropeptide FF receptor 2 × 1 (Q9Y5X5) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Morphine-modulating neuropeptide B × 1 (P15507) scfv16 × 1 Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.49 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 B; 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 Soluble cytochrome b562,Neuropeptide FF receptor 2,Neuropeptide FF receptor 2 × 1 (Q9Y5X5) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) Morphine-modulating neuropeptide B × 1 (P15507) scfv16 × 1 Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.49 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 3
Chains and sequence ranges Author chain G; PDBConstruct 1–71; UniProt 1–71

Morphine-modulating neuropeptide B

OrganismNot specified

UniProt P15507

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 L; UniProt 1–8 Non-standard monomer:Yes (specific site not provided by mmCIF) Soluble cytochrome b562,Neuropeptide FF receptor 2,Neuropeptide FF receptor 2 × 1 (Q9Y5X5) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) scfv16 × 1 Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.49 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 NPMB_BOVIN
Isoform
PDB entities 4
Chains and sequence ranges Author chain L; PDBConstruct 1–8; UniProt 1–8

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

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 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–354 Mutation:G203A,A326S Soluble cytochrome b562,Neuropeptide FF receptor 2,Neuropeptide FF receptor 2 × 1 (Q9Y5X5) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Morphine-modulating neuropeptide B × 1 (P15507) scfv16 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.49 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 1–354; UniProt 1–354

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 9m1o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9m1o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9m1o
Deposition date deposition_date2025-02-26
Structure title titleCryo-EM structures of NPFFR2 complex with neuropeptide FF
Keywords keywordsNPFFR2, NPFF, GPR74, GPCR, 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_guinier38.81
Radius of gyration Rg (electron density) rg_electron38.86
Forward intensity I(0) i0246243000.00
Molecular weight molecular_weight129310.0 kDa
Excluded volume excluded_volume162620 ų
Envelope volume envelope_volume211890 ų
Hydration-shell volume shell_volume46998 ų
Envelope diameter envelope_diameter130.7
Shell Rg shell_rg42.40
Envelope Rg envelope_rg38.76
Shape Rg shape_rg38.88
Total Rg total_rg39.00
Total atoms total_atoms9085
Residues n_residues1164
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 dmax129.6
Rg (real space) rg_real38.82
Rg uncertainty (real space) rg_real_error1.09
I(0) (real space) i0_real2.4620e+08
I(0) uncertainty (real space) i0_real_error4.4280e+06
Rg (reciprocal space) rg_reciprocal38.82
I(0) (reciprocal space) i0_reciprocal246200000.0000
Solution quality estimate total_estimate0.8229
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.4
Skewness Skewness skewness0.245
Kurtosis Kurtosis kurtosis-0.584
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha33170000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)