6qno

Rhodopsin-Gi protein complex

Method: ELECTRON MICROSCOPY Dmax: 147.9 Å Quality: GOOD

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

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 Other combination Heteromer Protein × 6 其他Polymer 1 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–354 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) Guanine nucleotide-binding protein G(T) subunit gamma-T1 × 1 (P02698) Fab antibody fragment light chain × 1 Fab antibody fragment heavy chain × 1 Rhodopsin × 1 (P02699) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 RET RETINAL × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;The detergent lauryl-maltose neopentyl glycol (LMNG) was used before the last purification step by gel filtration. In the gel filtration, detergent-free buffer was used. cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.38 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 1
Chains and sequence ranges Author chain A; PDBConstruct 23–376; UniProt 1–354

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

OrganismNot specified

UniProt P62871

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 6 其他Polymer 1 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 1–340 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(T) subunit gamma-T1 × 1 (P02698) Fab antibody fragment light chain × 1 Fab antibody fragment heavy chain × 1 Rhodopsin × 1 (P02699) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 RET RETINAL × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;The detergent lauryl-maltose neopentyl glycol (LMNG) was used before the last purification step by gel filtration. In the gel filtration, detergent-free buffer was used. cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.38 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.

72 other PDB entries and 73 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_BOVIN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–340; UniProt 1–340

Guanine nucleotide-binding protein G(T) subunit gamma-T1

OrganismNot specified

UniProt P02698

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 6 其他Polymer 1 PDB declaration: hexameric(6) Consistent with protein copy count Chain G; UniProt 1–74 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 (P62871) Fab antibody fragment light chain × 1 Fab antibody fragment heavy chain × 1 Rhodopsin × 1 (P02699) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 RET RETINAL × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;The detergent lauryl-maltose neopentyl glycol (LMNG) was used before the last purification step by gel filtration. In the gel filtration, detergent-free buffer was used. cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.38 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.

16 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG1_BOVIN
Isoform
PDB entities 3
Chains and sequence ranges Author chain G; PDBConstruct 1–74; UniProt 1–74

Rhodopsin

Bos taurus

UniProt P02699

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 6 其他Polymer 1 PDB declaration: hexameric(6) Consistent with protein copy count Chain R; UniProt 1–348 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 (P62871) Guanine nucleotide-binding protein G(T) subunit gamma-T1 × 1 (P02698) Fab antibody fragment light chain × 1 Fab antibody fragment heavy chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 RET RETINAL × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;The detergent lauryl-maltose neopentyl glycol (LMNG) was used before the last purification step by gel filtration. In the gel filtration, detergent-free buffer was used. cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.38 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.

74 other PDB entries and 95 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OPSD_BOVIN
Isoform
PDB entities 6
Chains and sequence ranges Author chain R; PDBConstruct 1–348; UniProt 1–348

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 6qno

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6qno
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6qno
Deposition date deposition_date2019-02-11
Structure title titleRhodopsin-Gi protein complex
Keywords keywordsGPCR and G protein complex, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier44.20
Radius of gyration Rg (electron density) rg_electron44.37
Forward intensity I(0) i0326014000.00
Molecular weight molecular_weight148360.0 kDa
Excluded volume excluded_volume185750 ų
Envelope volume envelope_volume261240 ų
Hydration-shell volume shell_volume52059 ų
Envelope diameter envelope_diameter147.9
Shell Rg shell_rg45.44
Envelope Rg envelope_rg44.01
Shape Rg shape_rg44.37
Total Rg total_rg44.43
Total atoms total_atoms10423
Residues n_residues1332
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 dmax147.9
Rg (real space) rg_real44.42
Rg uncertainty (real space) rg_real_error1.29
I(0) (real space) i0_real3.2600e+08
I(0) uncertainty (real space) i0_real_error6.0260e+06
Rg (reciprocal space) rg_reciprocal44.20
I(0) (reciprocal space) i0_reciprocal325900000.0000
Solution quality estimate total_estimate0.8609
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.2
Skewness Skewness skewness0.380
Kurtosis Kurtosis kurtosis-0.546
Angular range angular_range— – 0.1800 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha30140000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.886; Smooth: 0.627

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

8. Citations (1)

9. Files and Curves (10)