9pxy

Primed-state naloxone-mu opioid receptor-Gi GDPbS complex (rebound)

Method: ELECTRON MICROSCOPY Dmax: 121.3 Å Quality: GOOD

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

Soluble cytochrome b562,Mu-type opioid receptor,Soluble cytochrome b562,Mu-type opioid receptor,Mu opioid receptor

Homo sapiens

UniProt P0ABE7

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain R; UniProt 23–127 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 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) CLR CHOLESTEROL × 2 A1APV Naloxone × 1 VSN 5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]guanosine × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 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.

714 other PDB entries and 822 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C562_ECOLX
Isoform
PDB entities 1
Chains and sequence ranges Author chain R; PDBConstruct 62–166; UniProt 23–127

Soluble cytochrome b562,Mu-type opioid receptor,Soluble cytochrome b562,Mu-type opioid receptor,Mu 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 Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain R; UniProt 2–400 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 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) CLR CHOLESTEROL × 2 A1APV Naloxone × 1 VSN 5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]guanosine × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 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.

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 172–570; UniProt 2–400

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–354 Not recorded Soluble cytochrome b562,Mu-type opioid receptor,Soluble cytochrome b562,Mu-type opioid receptor,Mu opioid receptor × 1 (P0ABE7,P35372) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) CLR CHOLESTEROL × 2 A1APV Naloxone × 1 VSN 5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]guanosine × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 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 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

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Soluble cytochrome b562,Mu-type opioid receptor,Soluble cytochrome b562,Mu-type opioid receptor,Mu opioid receptor × 1 (P0ABE7,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 (P59768) CLR CHOLESTEROL × 2 A1APV Naloxone × 1 VSN 5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]guanosine × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 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.

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 3
Chains and sequence ranges Author chain B; PDBConstruct 23–361; UniProt 2–340

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

Homo sapiens

UniProt P59768

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 1–71 Not recorded Soluble cytochrome b562,Mu-type opioid receptor,Soluble cytochrome b562,Mu-type opioid receptor,Mu opioid receptor × 1 (P0ABE7,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 (P62873) CLR CHOLESTEROL × 2 A1APV Naloxone × 1 VSN 5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]guanosine × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 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.

1233 other PDB entries and 1236 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG2_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain C; PDBConstruct 1–71; UniProt 1–71

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 9pxy

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9pxy
Deposition date deposition_date2025-08-06
Structure title titlePrimed-state naloxone-mu opioid receptor-Gi GDPbS complex (rebound)
Keywords keywordsG protein coupled receptor, Mu Opioid receptor, Naloxone, MEMBRANE PROTEIN, GDP; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier35.78
Radius of gyration Rg (electron density) rg_electron36.08
Forward intensity I(0) i0204131000.00
Molecular weight molecular_weight116390.0 kDa
Excluded volume excluded_volume146310 ų
Envelope volume envelope_volume194750 ų
Hydration-shell volume shell_volume46303 ų
Envelope diameter envelope_diameter130.2
Shell Rg shell_rg40.73
Envelope Rg envelope_rg36.35
Shape Rg shape_rg36.08
Total Rg total_rg36.41
Total atoms total_atoms8160
Residues n_residues1020
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 dmax121.3
Rg (real space) rg_real35.88
Rg uncertainty (real space) rg_real_error1.07
I(0) (real space) i0_real2.0410e+08
I(0) uncertainty (real space) i0_real_error3.8410e+06
Rg (reciprocal space) rg_reciprocal35.82
I(0) (reciprocal space) i0_reciprocal204100000.0000
Solution quality estimate total_estimate0.8656
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary44.1
Skewness Skewness skewness0.431
Kurtosis Kurtosis kurtosis-0.177
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha52170000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.752

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)