6k42

cryo-EM structure of alpha2BAR-Gi1 complex

Method: ELECTRON MICROSCOPY Dmax: 119.9 Å Quality: GOOD

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

Guanine nucleotide-binding protein G(i) subunit alpha-1

Bos taurus

UniProt P63097

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 × 5 PDB declaration: pentameric(5) 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 (P62874) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Alpha-2A adrenergic receptor,Endolysin,Alpha-2B adrenergic receptor,Alpha-2B adrenergic receptor × 1 (P08913,A0A097J809,P18089) scFv × 1 CZX 4-[(1~{S})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.10 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.

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAI1_BOVIN
Isoform
PDB entities 1
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

Mus musculus

UniProt P62874

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63097) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Alpha-2A adrenergic receptor,Endolysin,Alpha-2B adrenergic receptor,Alpha-2B adrenergic receptor × 1 (P08913,A0A097J809,P18089) scFv × 1 CZX 4-[(1~{S})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.10 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.

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

View Construct and Data Evidence
UniProt name GBB1_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 12–350; 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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 1–71 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63097) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62874) Alpha-2A adrenergic receptor,Endolysin,Alpha-2B adrenergic receptor,Alpha-2B adrenergic receptor × 1 (P08913,A0A097J809,P18089) scFv × 1 CZX 4-[(1~{S})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.10 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 3
Chains and sequence ranges Author chain G; PDBConstruct 1–71; UniProt 1–71

Alpha-2A adrenergic receptor,Endolysin,Alpha-2B adrenergic receptor,Alpha-2B adrenergic receptor

Homo sapiens

UniProt A0A097J809

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 2–161 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63097) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62874) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) scFv × 1 CZX 4-[(1~{S})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.10 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 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A097J809_BPT4
Isoform
PDB entities 4
Chains and sequence ranges Author chain R; PDBConstruct 46–205; UniProt 2–161

Alpha-2A adrenergic receptor,Endolysin,Alpha-2B adrenergic receptor,Alpha-2B adrenergic receptor

Homo sapiens

UniProt P08913

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 1–27 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63097) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62874) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) scFv × 1 CZX 4-[(1~{S})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.10 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 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ADA2A_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain R; PDBConstruct 12–38; UniProt 1–27

Alpha-2A adrenergic receptor,Endolysin,Alpha-2B adrenergic receptor,Alpha-2B adrenergic receptor

Homo sapiens

UniProt P18089

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 7–217 Chain R; UniProt 355–450 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63097) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62874) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) scFv × 1 CZX 4-[(1~{S})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.10 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 ADA2B_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain R; PDBConstruct 206–416; UniProt 7–217 Author chain R; PDBConstruct 417–512; UniProt 355–450

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 6k42

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6k42
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6k42
Deposition date deposition_date2019-05-23
Structure title titlecryo-EM structure of alpha2BAR-Gi1 complex
Keywords keywordsGPCR, Complex, cryo-EM, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier36.90
Radius of gyration Rg (electron density) rg_electron36.72
Forward intensity I(0) i0235018000.00
Molecular weight molecular_weight125260.0 kDa
Excluded volume excluded_volume157450 ų
Envelope volume envelope_volume219500 ų
Hydration-shell volume shell_volume50188 ų
Envelope diameter envelope_diameter124.5
Shell Rg shell_rg42.24
Envelope Rg envelope_rg36.74
Shape Rg shape_rg36.71
Total Rg total_rg37.15
Total atoms total_atoms8808
Residues n_residues1116
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 dmax119.9
Rg (real space) rg_real36.81
Rg uncertainty (real space) rg_real_error0.76
I(0) (real space) i0_real2.3500e+08
I(0) uncertainty (real space) i0_real_error4.2460e+06
Rg (reciprocal space) rg_reciprocal36.87
I(0) (reciprocal space) i0_reciprocal235000000.0000
Solution quality estimate total_estimate0.8975
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.4
Skewness Skewness skewness0.203
Kurtosis Kurtosis kurtosis-0.528
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0003
Highest regularization parameter α highest_alpha58490000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.914

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)