8k9k

Full agonist-bound mu-type opioid receptor-G protein complex

Method: ELECTRON MICROSCOPY Dmax: 120.0 Å Quality: GOOD

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

Soluble cytochrome b562,Mu-type 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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain R; UniProt 23–128 Mutation:M7W,H102I,R106L DAMGO × 1 G protein subunit alpha i3 × 1 (F6VL43) Guanine nucleotide binding protein, beta polypeptide 1 × 1 (M1ERZ7) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) scFv16 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.98 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 23–128; UniProt 23–128

Soluble cytochrome b562,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 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain R; UniProt 64–362 Mutation:M7W,H102I,R106L DAMGO × 1 G protein subunit alpha i3 × 1 (F6VL43) Guanine nucleotide binding protein, beta polypeptide 1 × 1 (M1ERZ7) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) scFv16 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.98 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 139–437; UniProt 64–362

G protein subunit alpha i3

Macaca mulatta

UniProt F6VL43

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 1–354 Not recorded Soluble cytochrome b562,Mu-type opioid receptor × 1 (P0ABE7,P35372) DAMGO × 1 Guanine nucleotide binding protein, beta polypeptide 1 × 1 (M1ERZ7) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) scFv16 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.98 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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name F6VL43_MACMU
Isoform
PDB entities 3
Chains and sequence ranges Author chain A; PDBConstruct 1–354; UniProt 1–354

Guanine nucleotide binding protein, beta polypeptide 1

Homo sapiens

UniProt M1ERZ7

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 11–348 Not recorded Soluble cytochrome b562,Mu-type opioid receptor × 1 (P0ABE7,P35372) DAMGO × 1 G protein subunit alpha i3 × 1 (F6VL43) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) scFv16 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.98 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 M1ERZ7_MUSPF
Isoform
PDB entities 4
Chains and sequence ranges Author chain B; PDBConstruct 10–347; UniProt 11–348

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain G; UniProt 1–71 Not recorded Soluble cytochrome b562,Mu-type opioid receptor × 1 (P0ABE7,P35372) DAMGO × 1 G protein subunit alpha i3 × 1 (F6VL43) Guanine nucleotide binding protein, beta polypeptide 1 × 1 (M1ERZ7) scFv16 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.98 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 5
Chains and sequence ranges Author chain G; 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 8k9k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8k9k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8k9k
Deposition date deposition_date2023-08-01
Structure title titleFull agonist-bound mu-type opioid receptor-G protein complex
Keywords keywordsSIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier37.34
Radius of gyration Rg (electron density) rg_electron37.28
Forward intensity I(0) i0239535000.00
Molecular weight molecular_weight126470.0 kDa
Excluded volume excluded_volume158720 ų
Envelope volume envelope_volume207960 ų
Hydration-shell volume shell_volume47381 ų
Envelope diameter envelope_diameter124.7
Shell Rg shell_rg42.11
Envelope Rg envelope_rg37.26
Shape Rg shape_rg37.26
Total Rg total_rg37.64
Total atoms total_atoms8875
Residues n_residues1140
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 dmax120.0
Rg (real space) rg_real37.27
Rg uncertainty (real space) rg_real_error0.83
I(0) (real space) i0_real2.3950e+08
I(0) uncertainty (real space) i0_real_error3.7860e+06
Rg (reciprocal space) rg_reciprocal37.32
I(0) (reciprocal space) i0_reciprocal239500000.0000
Solution quality estimate total_estimate0.8977
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary51.4
Skewness Skewness skewness0.190
Kurtosis Kurtosis kurtosis-0.585
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha38610000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.851

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)