8zbe

cryo-EM structure of the octreotide-bound SSTR5-Gi complex

Method: ELECTRON MICROSCOPY Dmax: 117.8 Å Quality: REASONABLE

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

Beta-2 adrenergic receptor,Somatostatin receptor type 5,lgbit (fusion protein)

Oplophorus gracilirostris

UniProt P07550

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 1–24 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein subunit gamma × 1 (A0A9X9ZA26) ScFv16 × 1 octreotide × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.24 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.

143 other PDB entries and 145 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ADRB2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 25–48; UniProt 1–24

Beta-2 adrenergic receptor,Somatostatin receptor type 5,lgbit (fusion protein)

Oplophorus gracilirostris

UniProt P35346

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 1–364 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein subunit gamma × 1 (A0A9X9ZA26) ScFv16 × 1 octreotide × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.24 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.

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SSR5_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 49–412; UniProt 1–364

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 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 1–354 Not recorded Beta-2 adrenergic receptor,Somatostatin receptor type 5,lgbit (fusion protein) × 1 (P07550,P35346) Guanine nucleotide-binding protein subunit gamma × 1 (A0A9X9ZA26) ScFv16 × 1 octreotide × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.24 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 2
Chains and sequence ranges Author chain B; PDBConstruct 1–354; UniProt 1–354

Guanine nucleotide-binding protein subunit gamma

Rattus norvegicus

UniProt A0A9X9ZA26

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 D; UniProt 1–71 Not recorded Beta-2 adrenergic receptor,Somatostatin receptor type 5,lgbit (fusion protein) × 1 (P07550,P35346) Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) ScFv16 × 1 octreotide × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.24 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 A0A9X9ZA26_RAT
Isoform
PDB entities 3
Chains and sequence ranges Author chain D; PDBConstruct 1–71; UniProt 1–71

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 C; UniProt 2–340 Not recorded Beta-2 adrenergic receptor,Somatostatin receptor type 5,lgbit (fusion protein) × 1 (P07550,P35346) Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein subunit gamma × 1 (A0A9X9ZA26) ScFv16 × 1 octreotide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.24 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 6
Chains and sequence ranges Author chain C; PDBConstruct 13–351; UniProt 2–340

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 8zbe

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8zbe
Deposition date deposition_date2024-04-26
Structure title titlecryo-EM structure of the octreotide-bound SSTR5-Gi complex
Keywords keywordsSSTR5, octreoitde, structural protein, 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_guinier35.98
Radius of gyration Rg (electron density) rg_electron35.61
Forward intensity I(0) i0191296000.00
Molecular weight molecular_weight106040.0 kDa
Excluded volume excluded_volume130210 ų
Envelope volume envelope_volume181500 ų
Hydration-shell volume shell_volume43562 ų
Envelope diameter envelope_diameter119.6
Shell Rg shell_rg40.57
Envelope Rg envelope_rg35.90
Shape Rg shape_rg35.61
Total Rg total_rg35.93
Total atoms total_atoms7489
Residues n_residues1113
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 dmax117.8
Rg (real space) rg_real35.93
Rg uncertainty (real space) rg_real_error0.99
I(0) (real space) i0_real1.9130e+08
I(0) uncertainty (real space) i0_real_error3.4750e+06
Rg (reciprocal space) rg_reciprocal35.96
I(0) (reciprocal space) i0_reciprocal191300000.0000
Solution quality estimate total_estimate0.6909
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.5
Skewness Skewness skewness0.205
Kurtosis Kurtosis kurtosis-0.607
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha38500000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 0.101; Positv: 1.000; Valcen: 0.978; Smooth: 0.931

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)