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8sob

Phosphoinositide phosphate 3 kinase gamma bound with ADP

Method: ELECTRON MICROSCOPY Dmax: 147.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

phosphatidylinositol-4,5-bisphosphate 3-kinase

Sus scrofa

UniProt A0A8D1WUA4

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 2–1102 Not recorded Phosphoinositide 3-kinase regulatory subunit 5 × 1 （A0A8D0T2D6） ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE；Blot force 2 Resolution 3.90 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.

Other PDB Difference from Current Entry 8SOB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8SO9 Phosphoinositide phosphate 3 kinase gamma Deposited 2023-04-28 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–1102（1101 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Blot force 2
Resolution 3.03 Å
8SOA Phosphoinositide phosphate 3 kinase gamma bound with ATP Deposited 2023-04-28 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–1102（1101 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Blot force 2
Resolution 3.32 Å
8SOC Phosphoinositide phosphate 3 kinase gamma bound with ADP and Gbetagamma Deposited 2023-04-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 2–1102（1101 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Blot force 2
Resolution 3.50 Å
8SOD Phosphoinositide phosphate 3 kinase gamma bound with ADP and two Gbetagamma subunits in State 1 Deposited 2023-04-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 2–1102（1101 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Blot force 2
Resolution 3.40 Å
8SOE Phosphoinositide phosphate 3 kinase gamma bound with ADP and two Gbetagamma subunits in State 2 Deposited 2023-04-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 2–1102（1101 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Blot force 2
Resolution 3.60 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A8D1WUA4_PIG
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–1108； UniProt 2–1102

Phosphoinositide 3-kinase regulatory subunit 5

Sus scrofa

UniProt A0A8D0T2D6

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–877 Not recorded phosphatidylinositol-4,5-bisphosphate 3-kinase × 1 （A0A8D1WUA4） ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE；Blot force 2 Resolution 3.90 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.

Other PDB Difference from Current Entry 8SOB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8SO9 Phosphoinositide phosphate 3 kinase gamma Deposited 2023-04-28 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–877（877 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Blot force 2
Resolution 3.03 Å
8SOA Phosphoinositide phosphate 3 kinase gamma bound with ATP Deposited 2023-04-28 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–877（877 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Blot force 2
Resolution 3.32 Å
8SOC Phosphoinositide phosphate 3 kinase gamma bound with ADP and Gbetagamma Deposited 2023-04-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–877（877 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Blot force 2
Resolution 3.50 Å
8SOD Phosphoinositide phosphate 3 kinase gamma bound with ADP and two Gbetagamma subunits in State 1 Deposited 2023-04-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–877（877 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Blot force 2
Resolution 3.40 Å
8SOE Phosphoinositide phosphate 3 kinase gamma bound with ADP and two Gbetagamma subunits in State 2 Deposited 2023-04-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–877（877 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Blot force 2
Resolution 3.60 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A8D0T2D6_PIG
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–877； UniProt 1–877

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 8sob

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8sob
Deposition date deposition_date2023-04-28
Structure title titlePhosphoinositide phosphate 3 kinase gamma bound with ADP
Keywords keywordsPhosphoinositide 3-Kinase, Chemotaxis, Cancer, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier43.06 Å
Radius of gyration Rg (electron density) rg_electron43.01 Å
Forward intensity I(0) i0419387000.00
Molecular weight molecular_weight172700.0 kDa
Excluded volume excluded_volume218330 ų
Envelope volume envelope_volume305440 ų
Hydration-shell volume shell_volume61000 ų
Envelope diameter envelope_diameter146.6 Å
Shell Rg shell_rg46.29 Å
Envelope Rg envelope_rg42.37 Å
Shape Rg shape_rg42.98 Å
Total Rg total_rg43.28 Å
Total atoms total_atoms24428
Residues n_residues1507
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax147.6 Å
Rg (real space) rg_real43.20 Å
Rg uncertainty (real space) rg_real_error1.82 Å
I(0) (real space) i0_real4.1940e+08
I(0) uncertainty (real space) i0_real_error8.5630e+06
Rg (reciprocal space) rg_reciprocal43.06 Å
I(0) (reciprocal space) i0_reciprocal419300000.0000
Solution quality estimate total_estimate0.8684
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary47.9 Å
Skewness Skewness skewness0.437
Kurtosis Kurtosis kurtosis-0.360
Angular range angular_range— – 0.1850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha49900000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.806; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.885
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)