8f7s

Gi bound delta-opioid receptor in complex with deltorphin

Method: ELECTRON MICROSCOPY Dmax: 139.5 Å Quality: GOOD

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

Delta-type opioid receptor

Homo sapiens

UniProt P41143

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain D; UniProt 2–372 Chain R; UniProt 2–372 Not recorded deltorphin × 2 (P21850) Guanine nucleotide-binding protein G(i) subunit alpha-1 × 2 (P63096) 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) CLR CHOLESTEROL × 5 PLM PALMITIC ACID × 12 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 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 OPRD_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain D; PDBConstruct 12–382; UniProt 2–372 Author chain R; PDBConstruct 12–382; UniProt 2–372

deltorphin

OrganismNot specified

UniProt P21850

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain P; UniProt 107–113 Chain Q; UniProt 107–113 Fragment:UNP residues 107-113 Non-standard monomer:Yes (specific site not provided by mmCIF) Delta-type opioid receptor × 2 (P41143) Guanine nucleotide-binding protein G(i) subunit alpha-1 × 2 (P63096) 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) CLR CHOLESTEROL × 5 PLM PALMITIC ACID × 12 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 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 DA2D_PHYBI
Isoform
PDB entities 2
Chains and sequence ranges Author chain P; PDBConstruct 1–7; UniProt 107–113 Author chain Q; PDBConstruct 1–7; UniProt 107–113

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 1–354 Chain F; UniProt 1–354 Not recorded Delta-type opioid receptor × 2 (P41143) deltorphin × 2 (P21850) 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) CLR CHOLESTEROL × 5 PLM PALMITIC ACID × 12 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 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 3
Chains and sequence ranges Author chain A; PDBConstruct 1–354; UniProt 1–354 Author chain F; PDBConstruct 1–354; UniProt 1–354

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Delta-type opioid receptor × 2 (P41143) deltorphin × 2 (P21850) Guanine nucleotide-binding protein G(i) subunit alpha-1 × 2 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) CLR CHOLESTEROL × 5 PLM PALMITIC ACID × 12 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 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 15–353; 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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain C; UniProt 1–68 Not recorded Delta-type opioid receptor × 2 (P41143) deltorphin × 2 (P21850) Guanine nucleotide-binding protein G(i) subunit alpha-1 × 2 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) CLR CHOLESTEROL × 5 PLM PALMITIC ACID × 12 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 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 C; PDBConstruct 1–68; UniProt 1–68

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 8f7s

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8f7s
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8f7s
Deposition date deposition_date2022-11-20
Structure title titleGi bound delta-opioid receptor in complex with deltorphin
Keywords keywordsdelta opioid receptor, G protein coupled receptor, deltorphin, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier41.03
Radius of gyration Rg (electron density) rg_electron40.71
Forward intensity I(0) i0259251000.00
Molecular weight molecular_weight142220.0 kDa
Excluded volume excluded_volume182800 ų
Envelope volume envelope_volume252370 ų
Hydration-shell volume shell_volume52961 ų
Envelope diameter envelope_diameter142.8
Shell Rg shell_rg44.96
Envelope Rg envelope_rg40.48
Shape Rg shape_rg40.69
Total Rg total_rg41.05
Total atoms total_atoms9975
Residues n_residues1225
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 dmax139.5
Rg (real space) rg_real41.18
Rg uncertainty (real space) rg_real_error1.29
I(0) (real space) i0_real2.5930e+08
I(0) uncertainty (real space) i0_real_error4.3630e+06
Rg (reciprocal space) rg_reciprocal41.03
I(0) (reciprocal space) i0_reciprocal259200000.0000
Solution quality estimate total_estimate0.8679
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.0
Skewness Skewness skewness0.401
Kurtosis Kurtosis kurtosis-0.489
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22950000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.801

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id8f7sB01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

8. Citations (1)

9. Files and Curves (10)