8iod

Cryo-EM structure of the PG-901-bound human melanocortin receptor 5 (MC5R)-Gs complex

Method: ELECTRON MICROSCOPY Dmax: 114.2 Å Quality: GOOD

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

Guanine nucleotide-binding protein G(i) subunit alpha-1,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 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 26–66 Chain A; UniProt 204–394 Mutation:G49D,E50N,L63Y,ten mutations and A249D,S252D,L272D,I372A,V375I,G226A,A366S Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,HiBiT × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) PG-901 × 1 Nanobody-35 × 1 HA signal peptide,Melanocortin receptor 5,LgBiT subunit × 1 (P03435,P33032) CA CALCIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.59 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
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 19–59; UniProt 26–66 Author chain A; PDBConstruct 181–361; UniProt 204–394

Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

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 1–18 Chain A; UniProt 60–180 Mutation:G49D,E50N,L63Y,ten mutations and A249D,S252D,L272D,I372A,V375I,G226A,A366S Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,HiBiT × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) PG-901 × 1 Nanobody-35 × 1 HA signal peptide,Melanocortin receptor 5,LgBiT subunit × 1 (P03435,P33032) CA CALCIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.59 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 1
Chains and sequence ranges Author chain A; PDBConstruct 1–18; UniProt 1–18 Author chain A; PDBConstruct 60–180; UniProt 60–180

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

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 Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63096,P63092) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) PG-901 × 1 Nanobody-35 × 1 HA signal peptide,Melanocortin receptor 5,LgBiT subunit × 1 (P03435,P33032) CA CALCIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.59 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 7–345; 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 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain G; UniProt 1–71 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63096,P63092) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,HiBiT × 1 (P62873) PG-901 × 1 Nanobody-35 × 1 HA signal peptide,Melanocortin receptor 5,LgBiT subunit × 1 (P03435,P33032) CA CALCIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.59 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

HA signal peptide,Melanocortin receptor 5,LgBiT subunit

Homo sapiens

UniProt P03435

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 1–16 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63096,P63092) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,HiBiT × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) PG-901 × 1 Nanobody-35 × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.59 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.

15 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HEMA_I75A3
Isoform
PDB entities 6
Chains and sequence ranges Author chain R; PDBConstruct 1–16; UniProt 1–16

HA signal peptide,Melanocortin receptor 5,LgBiT subunit

Homo sapiens

UniProt P33032

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 2–325 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63096,P63092) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,HiBiT × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) PG-901 × 1 Nanobody-35 × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.59 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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MC5R_HUMAN
Isoform
PDB entities 6
Chains and sequence ranges Author chain R; PDBConstruct 17–340; UniProt 2–325

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 8iod

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8iod
Deposition date deposition_date2023-03-10
Structure title titleCryo-EM structure of the PG-901-bound human melanocortin receptor 5 (MC5R)-Gs complex
Keywords keywordshuman melanocortin receptor 5, G protein-coupled receptor, PG-901, membrane protein; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier33.91
Radius of gyration Rg (electron density) rg_electron33.93
Forward intensity I(0) i0206129000.00
Molecular weight molecular_weight114960.0 kDa
Excluded volume excluded_volume143750 ų
Envelope volume envelope_volume183890 ų
Hydration-shell volume shell_volume45419 ų
Envelope diameter envelope_diameter121.4
Shell Rg shell_rg40.04
Envelope Rg envelope_rg34.41
Shape Rg shape_rg33.90
Total Rg total_rg34.48
Total atoms total_atoms8061
Residues n_residues1021
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 dmax114.2
Rg (real space) rg_real33.98
Rg uncertainty (real space) rg_real_error0.95
I(0) (real space) i0_real2.0610e+08
I(0) uncertainty (real space) i0_real_error3.5950e+06
Rg (reciprocal space) rg_reciprocal33.94
I(0) (reciprocal space) i0_reciprocal206100000.0000
Solution quality estimate total_estimate0.8668
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.4
Skewness Skewness skewness0.445
Kurtosis Kurtosis kurtosis-0.198
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha44240000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.793

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)