8qeg

Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor

Method: X-RAY DIFFRACTION Dmax: 95.1 Å Quality: EXCELLENT

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

Guanine nucleotide-binding protein subunit alpha-11

Homo sapiens

UniProt P29992

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 36–359 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) GDP GUANOSINE-5'-DIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 8 DAM N-METHYL-ALPHA-BETA-DEHYDROALANINE × 1 HF2 (2R)-2-hydroxy-3-phenylpropanoic acid × 1 THC N-METHYLCARBONYLTHREONINE × 1 OTH N,O-dimethyl-L-threonine × 1 HL2 (2S,3R)-2-amino-3-hydroxy-4-methylpentanoic acid × 2 MAA N-methyl-L-alanine × 1 ALA ALANINE × 1 ACE ACETYL GROUP × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4.5;277 K;0.09 M Na Acetate pH 4.5, 2.7 % PEG Smears Medium, 6.3 % MPD, 0.5 n-octyl-beta-D-Glucoside and 3% D-Trehalose Resolution 1.70 Å R-free 0.188

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.

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNA11_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 29–352; UniProt 36–359

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

Homo sapiens

UniProt P62873

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Guanine nucleotide-binding protein subunit alpha-11 × 1 (P29992) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) GDP GUANOSINE-5'-DIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 8 DAM N-METHYL-ALPHA-BETA-DEHYDROALANINE × 1 HF2 (2R)-2-hydroxy-3-phenylpropanoic acid × 1 THC N-METHYLCARBONYLTHREONINE × 1 OTH N,O-dimethyl-L-threonine × 1 HL2 (2S,3R)-2-amino-3-hydroxy-4-methylpentanoic acid × 2 MAA N-methyl-L-alanine × 1 ALA ALANINE × 1 ACE ACETYL GROUP × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4.5;277 K;0.09 M Na Acetate pH 4.5, 2.7 % PEG Smears Medium, 6.3 % MPD, 0.5 n-octyl-beta-D-Glucoside and 3% D-Trehalose Resolution 1.70 Å R-free 0.188

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.

1260 other PDB entries and 1263 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 6–344; 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 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain G; UniProt 1–71 Mutation:C68S Guanine nucleotide-binding protein subunit alpha-11 × 1 (P29992) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) GDP GUANOSINE-5'-DIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 8 DAM N-METHYL-ALPHA-BETA-DEHYDROALANINE × 1 HF2 (2R)-2-hydroxy-3-phenylpropanoic acid × 1 THC N-METHYLCARBONYLTHREONINE × 1 OTH N,O-dimethyl-L-threonine × 1 HL2 (2S,3R)-2-amino-3-hydroxy-4-methylpentanoic acid × 2 MAA N-methyl-L-alanine × 1 ALA ALANINE × 1 ACE ACETYL GROUP × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4.5;277 K;0.09 M Na Acetate pH 4.5, 2.7 % PEG Smears Medium, 6.3 % MPD, 0.5 n-octyl-beta-D-Glucoside and 3% D-Trehalose Resolution 1.70 Å R-free 0.188

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

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 8qeg

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8qeg
Deposition date deposition_date2023-08-31
Structure title titleCrystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor
Keywords keywordsG protein, YM-254890, cell signaling, GNA11, GNB1, GNG2, G alpha 11, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.79
Radius of gyration Rg (electron density) rg_electron29.07
Forward intensity I(0) i0113571000.00
Molecular weight molecular_weight82941.0 kDa
Excluded volume excluded_volume103250 ų
Envelope volume envelope_volume128910 ų
Hydration-shell volume shell_volume36791 ų
Envelope diameter envelope_diameter98.5
Shell Rg shell_rg36.50
Envelope Rg envelope_rg28.94
Shape Rg shape_rg29.08
Total Rg total_rg29.71
Total atoms total_atoms5823
Residues n_residues726
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 dmax95.1
Rg (real space) rg_real29.74
Rg uncertainty (real space) rg_real_error0.48
I(0) (real space) i0_real1.1360e+08
I(0) uncertainty (real space) i0_real_error1.5650e+06
Rg (reciprocal space) rg_reciprocal29.76
I(0) (reciprocal space) i0_reciprocal113600000.0000
Solution quality estimate total_estimate0.9044
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.1
Skewness Skewness skewness0.267
Kurtosis Kurtosis kurtosis-0.533
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23270000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.962

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (14)

8. Citations (1)

9. Files and Curves (10)