6cmo

Rhodopsin-Gi complex

Method: ELECTRON MICROSCOPY Dmax: 158.5 Å Quality: GOOD

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

chimera protein of Soluble cytochrome b562 and Rhodopsin

Homo sapiens

UniProt P08100

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 其他Polymer 1 PDB declaration: hexameric(6) Consistent with protein copy count Chain R; UniProt 3–323 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) Fab light chain × 1 Fab Heavy chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.50 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.

3 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OPSD_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain R; PDBConstruct 143–463; UniProt 3–323

chimera protein of Soluble cytochrome b562 and Rhodopsin

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 其他Polymer 1 PDB declaration: hexameric(6) 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 (P54311) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Fab light chain × 1 Fab Heavy chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.50 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 35–139; UniProt 23–127

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 × 6 其他Polymer 1 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–354 Not recorded chimera protein of Soluble cytochrome b562 and Rhodopsin × 1 (P0ABE7,P08100) 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) Fab light chain × 1 Fab Heavy chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.50 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 Insufficient information Heteromer Protein × 6 其他Polymer 1 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded chimera protein of Soluble cytochrome b562 and Rhodopsin × 1 (P0ABE7,P08100) 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) Fab light chain × 1 Fab Heavy chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.50 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 7–345; 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 Insufficient information Heteromer Protein × 6 其他Polymer 1 PDB declaration: hexameric(6) Consistent with protein copy count Chain G; UniProt 1–68 Not recorded chimera protein of Soluble cytochrome b562 and Rhodopsin × 1 (P0ABE7,P08100) 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) Fab light chain × 1 Fab Heavy chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.50 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 G; 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 6cmo

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6cmo
Deposition date deposition_date2018-03-05
Structure title titleRhodopsin-Gi complex
Keywords keywordsRhodopsin; G protein; cryo-EM; Structure, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier46.72
Radius of gyration Rg (electron density) rg_electron47.69
Forward intensity I(0) i0421532000.00
Molecular weight molecular_weight168470.0 kDa
Excluded volume excluded_volume210870 ų
Envelope volume envelope_volume322470 ų
Hydration-shell volume shell_volume61536 ų
Envelope diameter envelope_diameter166.7
Shell Rg shell_rg46.54
Envelope Rg envelope_rg47.18
Shape Rg shape_rg47.70
Total Rg total_rg47.57
Total atoms total_atoms11834
Residues n_residues1516
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 dmax158.5
Rg (real space) rg_real47.17
Rg uncertainty (real space) rg_real_error1.69
I(0) (real space) i0_real4.2150e+08
I(0) uncertainty (real space) i0_real_error8.1810e+06
Rg (reciprocal space) rg_reciprocal46.73
I(0) (reciprocal space) i0_reciprocal421300000.0000
Solution quality estimate total_estimate0.8330
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary46.6
Skewness Skewness skewness0.559
Kurtosis Kurtosis kurtosis-0.194
Angular range angular_range— – 0.1700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha48110000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.819; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.403

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)