7piv

Active Melanocortin-4 receptor (MC4R)- Gs protein complex bound to agonist NDP-alpha-MSH at 2.86 A resolution.

Method: ELECTRON MICROSCOPY Dmax: 114.9 Å Quality: GOOD

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

Melanocortin receptor 4

Homo sapiens

UniProt P32245

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 1–332 Not recorded NDP-alpha-MSH (other names Afamelanotide; Scenesse) × 1 Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092) 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 (P63213) Camelid antibody VHH fragment - nanobody 35 × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.86 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.

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MC4R_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain R; PDBConstruct 9–340; UniProt 1–332

Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

Homo sapiens

UniProt P63092

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 1–380 Not recorded Melanocortin receptor 4 × 1 (P32245) NDP-alpha-MSH (other names Afamelanotide; Scenesse) × 1 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 (P63213) Camelid antibody VHH fragment - nanobody 35 × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.86 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.

348 other PDB entries and 356 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAS2_HUMAN
Isoform P63092-2
PDB entities 3
Chains and sequence ranges Author chain A; PDBConstruct 1–380; UniProt 1–380

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 Melanocortin receptor 4 × 1 (P32245) NDP-alpha-MSH (other names Afamelanotide; Scenesse) × 1 Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63213) Camelid antibody VHH fragment - nanobody 35 × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.86 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 4
Chains and sequence ranges Author chain B; PDBConstruct 7–345; UniProt 2–340

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

Mus musculus

UniProt P63213

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 Melanocortin receptor 4 × 1 (P32245) NDP-alpha-MSH (other names Afamelanotide; Scenesse) × 1 Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) Camelid antibody VHH fragment - nanobody 35 × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.86 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.

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG2_MOUSE
Isoform
PDB entities 5
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 7piv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7piv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7piv
Deposition date deposition_date2021-08-23
Structure title titleActive Melanocortin-4 receptor (MC4R)- Gs protein complex bound to agonist NDP-alpha-MSH at 2.86 A resolution.
Keywords keywords;GPCR, MELANOCORTIN-4 RECEPTOR, MELANOCORTIN RECEPTORS, SETMELANOTIDE, NDP-ALPHA-MSH, ALPHA-18 MSH, ANTAGONISM, AGONISM, APPETITE REGULATION, ANTI-OBESITY TREATMENT, SIGNALING PROTEIN ;; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier33.81
Radius of gyration Rg (electron density) rg_electron33.75
Forward intensity I(0) i0179400000.00
Molecular weight molecular_weight107830.0 kDa
Excluded volume excluded_volume135190 ų
Envelope volume envelope_volume173720 ų
Hydration-shell volume shell_volume43761 ų
Envelope diameter envelope_diameter124.3
Shell Rg shell_rg39.49
Envelope Rg envelope_rg33.92
Shape Rg shape_rg33.73
Total Rg total_rg34.27
Total atoms total_atoms7571
Residues n_residues975
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 dmax114.9
Rg (real space) rg_real33.92
Rg uncertainty (real space) rg_real_error0.88
I(0) (real space) i0_real1.7940e+08
I(0) uncertainty (real space) i0_real_error2.8220e+06
Rg (reciprocal space) rg_reciprocal33.85
I(0) (reciprocal space) i0_reciprocal179400000.0000
Solution quality estimate total_estimate0.8590
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary36.7
Skewness Skewness skewness0.481
Kurtosis Kurtosis kurtosis-0.170
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha45010000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.820; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.925; Smooth: 0.777

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id7pivB01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id7pivN01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)