9bjk

Inactive mu opioid receptor bound to Nb6, naloxone and NAM

Method: ELECTRON MICROSCOPY Dmax: 96.8 Å Quality: REASONABLE

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

Mu-type opioid receptor

Mus musculus

UniProt P42866

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain R; UniProt 6–398 Not recorded kappa opioid receptor Nanobody 6 × 1 A1APV Naloxone × 1 A1APU Nalpha-[({(1M)-1-[5-(benzyloxy)pyridin-3-yl]naphthalen-2-yl}sulfanyl)acetyl]-3-methoxy-N,4-dimethyl-L-phenylalaninamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.26 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.

26 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OPRM_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain R; PDBConstruct 26–418; UniProt 6–398

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 9bjk

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9bjk
Deposition date deposition_date2024-04-25
Structure title titleInactive mu opioid receptor bound to Nb6, naloxone and NAM
Keywords keywordsG-protein coupled receptor, inactive, opioid, allosteric modulator, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier25.18
Radius of gyration Rg (electron density) rg_electron24.23
Forward intensity I(0) i019198900.00
Molecular weight molecular_weight35755.0 kDa
Excluded volume excluded_volume45663 ų
Envelope volume envelope_volume57901 ų
Hydration-shell volume shell_volume21390 ų
Envelope diameter envelope_diameter100.7
Shell Rg shell_rg29.27
Envelope Rg envelope_rg25.51
Shape Rg shape_rg24.31
Total Rg total_rg24.62
Total atoms total_atoms2525
Residues n_residues338
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 dmax96.8
Rg (real space) rg_real25.47
Rg uncertainty (real space) rg_real_error1.13
I(0) (real space) i0_real1.9200e+07
I(0) uncertainty (real space) i0_real_error3.0600e+05
Rg (reciprocal space) rg_reciprocal25.38
I(0) (reciprocal space) i0_reciprocal19200000.0000
Solution quality estimate total_estimate0.7475
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.6
Skewness Skewness skewness0.682
Kurtosis Kurtosis kurtosis0.138
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2777000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.474; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.358; Smooth: 0.934

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)