8efb

Oliceridine-bound mu-opioid receptor-Gi complex

Method: ELECTRON MICROSCOPY Dmax: 122.5 Å Quality: GOOD

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

Mu-type opioid receptor

Homo sapiens

UniProt P35372

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 2–368 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (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) scFv16 × 1 WH2 N-[(3-methoxythiophen-2-yl)methyl]-2-[(9R)-9-(pyridin-2-yl)-6-oxaspiro[4.5]decan-9-yl]ethan-1-amine × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.20 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.

28 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OPRM_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain R; PDBConstruct 1–367; UniProt 2–368

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–354 Not recorded Mu-type opioid receptor × 1 (P35372) 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) scFv16 × 1 WH2 N-[(3-methoxythiophen-2-yl)methyl]-2-[(9R)-9-(pyridin-2-yl)-6-oxaspiro[4.5]decan-9-yl]ethan-1-amine × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.20 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 A; 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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Mu-type opioid receptor × 1 (P35372) Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) scFv16 × 1 WH2 N-[(3-methoxythiophen-2-yl)methyl]-2-[(9R)-9-(pyridin-2-yl)-6-oxaspiro[4.5]decan-9-yl]ethan-1-amine × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.20 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 3
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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 1–68 Not recorded Mu-type opioid receptor × 1 (P35372) Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) scFv16 × 1 WH2 N-[(3-methoxythiophen-2-yl)methyl]-2-[(9R)-9-(pyridin-2-yl)-6-oxaspiro[4.5]decan-9-yl]ethan-1-amine × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.20 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 4
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 8efb

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8efb
Deposition date deposition_date2022-09-08
Structure title titleOliceridine-bound mu-opioid receptor-Gi complex
Keywords keywordsmu-opioid receptor, G protein, oliceridine, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier37.51
Radius of gyration Rg (electron density) rg_electron37.51
Forward intensity I(0) i0243673000.00
Molecular weight molecular_weight127550.0 kDa
Excluded volume excluded_volume160100 ų
Envelope volume envelope_volume213640 ų
Hydration-shell volume shell_volume48301 ų
Envelope diameter envelope_diameter125.6
Shell Rg shell_rg42.35
Envelope Rg envelope_rg37.59
Shape Rg shape_rg37.50
Total Rg total_rg37.85
Total atoms total_atoms8947
Residues n_residues1136
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 dmax122.5
Rg (real space) rg_real37.46
Rg uncertainty (real space) rg_real_error0.93
I(0) (real space) i0_real2.4370e+08
I(0) uncertainty (real space) i0_real_error3.8430e+06
Rg (reciprocal space) rg_reciprocal37.50
I(0) (reciprocal space) i0_reciprocal243700000.0000
Solution quality estimate total_estimate0.8971
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary49.6
Skewness Skewness skewness0.212
Kurtosis Kurtosis kurtosis-0.578
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha47120000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.889

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id8efbB01
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_id8efbE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id8efbE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)