9k07

Cryo-EM structure of the DSO-5a-bound human BRS3-Gq complex

Method: ELECTRON MICROSCOPY Dmax: 123.6 Å Quality: EXCELLENT

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

Bombesin receptor subtype-3,Oplophorus-luciferin 2-monooxygenase catalytic subunit

Oplophorus gracilirostris

UniProt P32247

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 1–399 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P04899,P63092) scFv16 × 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 (P63212) Nanobody-35 × 1 A1EL6 [(1~{S})-1-[1,4-dimethoxy-8-nitroso-5-(oxidanylamino)naphthalen-2-yl]-2,2-dimethyl-but-3-enyl] furan-2-carboxylate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.83 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 BRS3_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain R; PDBConstruct 17–415; UniProt 1–399

Bombesin receptor subtype-3,Oplophorus-luciferin 2-monooxygenase catalytic subunit

Oplophorus gracilirostris

UniProt Q9GV45

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 28–183 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P04899,P63092) scFv16 × 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 (P63212) Nanobody-35 × 1 A1EL6 [(1~{S})-1-[1,4-dimethoxy-8-nitroso-5-(oxidanylamino)naphthalen-2-yl]-2,2-dimethyl-but-3-enyl] furan-2-carboxylate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.83 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.

21 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LUCI_OPLGR
Isoform
PDB entities 1
Chains and sequence ranges Author chain R; PDBConstruct 432–587; UniProt 28–183

Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

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 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–39 Not recorded Bombesin receptor subtype-3,Oplophorus-luciferin 2-monooxygenase catalytic subunit × 1 (P32247,Q9GV45) scFv16 × 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 (P63212) Nanobody-35 × 1 A1EL6 [(1~{S})-1-[1,4-dimethoxy-8-nitroso-5-(oxidanylamino)naphthalen-2-yl]-2,2-dimethyl-but-3-enyl] furan-2-carboxylate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.83 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 2
Chains and sequence ranges Author chain A; PDBConstruct 1–39; UniProt 1–39

Guanine nucleotide-binding protein G(i) subunit alpha-2,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 47–64 Chain A; UniProt 204–253 Chain A; UniProt 264–394 Not recorded Bombesin receptor subtype-3,Oplophorus-luciferin 2-monooxygenase catalytic subunit × 1 (P32247,Q9GV45) scFv16 × 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 (P63212) Nanobody-35 × 1 A1EL6 [(1~{S})-1-[1,4-dimethoxy-8-nitroso-5-(oxidanylamino)naphthalen-2-yl]-2,2-dimethyl-but-3-enyl] furan-2-carboxylate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.83 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 2
Chains and sequence ranges Author chain A; PDBConstruct 40–57; UniProt 47–64 Author chain A; PDBConstruct 66–115; UniProt 204–253 Author chain A; PDBConstruct 116–246; UniProt 264–394

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 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Bombesin receptor subtype-3,Oplophorus-luciferin 2-monooxygenase catalytic subunit × 1 (P32247,Q9GV45) Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P04899,P63092) scFv16 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Nanobody-35 × 1 A1EL6 [(1~{S})-1-[1,4-dimethoxy-8-nitroso-5-(oxidanylamino)naphthalen-2-yl]-2,2-dimethyl-but-3-enyl] furan-2-carboxylate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.83 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

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 2–71 Not recorded Bombesin receptor subtype-3,Oplophorus-luciferin 2-monooxygenase catalytic subunit × 1 (P32247,Q9GV45) Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P04899,P63092) scFv16 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) Nanobody-35 × 1 A1EL6 [(1~{S})-1-[1,4-dimethoxy-8-nitroso-5-(oxidanylamino)naphthalen-2-yl]-2,2-dimethyl-but-3-enyl] furan-2-carboxylate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.83 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 5
Chains and sequence ranges Author chain G; PDBConstruct 1–70; UniProt 2–71

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 9k07

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9k07
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9k07
Deposition date deposition_date2024-10-15
Structure title titleCryo-EM structure of the DSO-5a-bound human BRS3-Gq complex
Keywords keywordsDSO-5a, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier37.75
Radius of gyration Rg (electron density) rg_electron37.64
Forward intensity I(0) i0549684000.00
Molecular weight molecular_weight127100.0 kDa
Excluded volume excluded_volume122850 ų
Envelope volume envelope_volume221860 ų
Hydration-shell volume shell_volume50122 ų
Envelope diameter envelope_diameter125.2
Shell Rg shell_rg42.48
Envelope Rg envelope_rg37.60
Shape Rg shape_rg37.66
Total Rg total_rg37.82
Total atoms total_atoms9618
Residues n_residues1236
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 dmax123.6
Rg (real space) rg_real37.70
Rg uncertainty (real space) rg_real_error1.32
I(0) (real space) i0_real5.4970e+08
I(0) uncertainty (real space) i0_real_error9.7920e+06
Rg (reciprocal space) rg_reciprocal37.74
I(0) (reciprocal space) i0_reciprocal549700000.0000
Solution quality estimate total_estimate0.9032
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary44.1
Skewness Skewness skewness0.223
Kurtosis Kurtosis kurtosis-0.614
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha45850000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.958

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)