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6bq1

Human PI4KIIIa lipid kinase complex

Method: ELECTRON MICROSCOPY Dmax: 255.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Phosphatidylinositol 4-kinase III alpha (PI4KA)

Homo sapiens

UniProt P42356

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 932–2102 Chain E； UniProt 932–2102 Not recorded Tetratricopeptide repeat protein 7B × 2 （Q86TV6） Protein FAM126A × 2 （Q9BYI3） E4S 5-{2-amino-1-[4-(morpholin-4-yl)phenyl]-1H-benzimidazol-6-yl}-N-(2-fluorophenyl)-2-methoxypyridine-3-sulfonamide × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.60 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 6BQ1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9B9G Structure of the PI4KA complex bound to Calcineurin Deposited 2024-04-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 1–2102（2102 aa）
Chain B 1–2102（2102 aa）
Not recorded CA CALCIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；Freshly prepared gel filtration buffer, filtered through 0.22um filter and degassed
cryo-EM vitrification conditions Cryogen ETHANE；Blot force -5, blot time 1 s
Resolution 3.50 Å
9BAX PI4KA complex bound to C-terminus of EFR3A Deposited 2024-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–2102（2102 aa）
Chain B 1–2102（2102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7；Freshly prepared gel filtration buffer, filtered through 0.22um filter and degassed
cryo-EM vitrification conditions Cryogen ETHANE；Blot force -5, blot time 1.5 s
Resolution 3.65 Å
9OT6 Cryo-EM structure of the PI4KA complex bound to an EFR3 interfering nanobody (F3IN) Deposited 2025-05-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–2102（2102 aa）
Chain B 1–2102（2102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE；Blot force -5, blot time 1.5 s.
Resolution 3.54 Å

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

View Construct and Data Evidence
UniProt name PI4KA_HUMAN
Isoform —
PDB entities 1, 4
Chains and sequence ranges Author chain A； PDBConstruct 477–1647； UniProt 932–2102 Author chain E； PDBConstruct 478–1648； UniProt 932–2102

Tetratricopeptide repeat protein 7B

Homo sapiens

UniProt Q86TV6

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain B； UniProt 1–843 Chain F； UniProt 1–843 Not recorded Phosphatidylinositol 4-kinase III alpha (PI4KA) × 1 （P42356） Protein FAM126A × 2 （Q9BYI3） Phosphatidylinositol 4-kinase III alpha (PI4KA) × 1 （P42356） E4S 5-{2-amino-1-[4-(morpholin-4-yl)phenyl]-1H-benzimidazol-6-yl}-N-(2-fluorophenyl)-2-methoxypyridine-3-sulfonamide × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.60 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 6BQ1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5DSE Crystal Structure of the TTC7B/Hyccin Complex Deposited 2015-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 7–843（837 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.35 ul protein + 1.35 ul mother liquor (0.1 M HEPES [pH 7.0-7.4], 4-5% polyethylene glycol [PEG] 8,000) + 0.3 ul 0.2 M 3-(1-Pyridino)-1-propane sulfonate (NDSB-201)
Resolution 2.90 Å R-free 0.242
5DSE Crystal Structure of the TTC7B/Hyccin Complex Deposited 2015-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 7–843（837 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.35 ul protein + 1.35 ul mother liquor (0.1 M HEPES [pH 7.0-7.4], 4-5% polyethylene glycol [PEG] 8,000) + 0.3 ul 0.2 M 3-(1-Pyridino)-1-propane sulfonate (NDSB-201)
Resolution 2.90 Å R-free 0.242
9B9G Structure of the PI4KA complex bound to Calcineurin Deposited 2024-04-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain D 1–843（843 aa）
Chain F 1–843（843 aa）
Not recorded CA CALCIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；Freshly prepared gel filtration buffer, filtered through 0.22um filter and degassed
cryo-EM vitrification conditions Cryogen ETHANE；Blot force -5, blot time 1 s
Resolution 3.50 Å
9BAX PI4KA complex bound to C-terminus of EFR3A Deposited 2024-04-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–843（843 aa）
Chain F 1–843（843 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7；Freshly prepared gel filtration buffer, filtered through 0.22um filter and degassed
cryo-EM vitrification conditions Cryogen ETHANE；Blot force -5, blot time 1.5 s
Resolution 3.65 Å
9OT6 Cryo-EM structure of the PI4KA complex bound to an EFR3 interfering nanobody (F3IN) Deposited 2025-05-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–843（843 aa）
Chain F 1–843（843 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE；Blot force -5, blot time 1.5 s.
Resolution 3.54 Å

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

View Construct and Data Evidence
UniProt name TTC7B_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 21–863； UniProt 1–843 Author chain F； PDBConstruct 21–863； UniProt 1–843

Protein FAM126A

Homo sapiens

UniProt Q9BYI3

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain C； UniProt 2–289 Chain G； UniProt 2–289 Not recorded Phosphatidylinositol 4-kinase III alpha (PI4KA) × 1 （P42356） Tetratricopeptide repeat protein 7B × 2 （Q86TV6） Phosphatidylinositol 4-kinase III alpha (PI4KA) × 1 （P42356） E4S 5-{2-amino-1-[4-(morpholin-4-yl)phenyl]-1H-benzimidazol-6-yl}-N-(2-fluorophenyl)-2-methoxypyridine-3-sulfonamide × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.60 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 6BQ1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5DSE Crystal Structure of the TTC7B/Hyccin Complex Deposited 2015-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–308（307 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.35 ul protein + 1.35 ul mother liquor (0.1 M HEPES [pH 7.0-7.4], 4-5% polyethylene glycol [PEG] 8,000) + 0.3 ul 0.2 M 3-(1-Pyridino)-1-propane sulfonate (NDSB-201)
Resolution 2.90 Å R-free 0.242
5DSE Crystal Structure of the TTC7B/Hyccin Complex Deposited 2015-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–308（307 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.35 ul protein + 1.35 ul mother liquor (0.1 M HEPES [pH 7.0-7.4], 4-5% polyethylene glycol [PEG] 8,000) + 0.3 ul 0.2 M 3-(1-Pyridino)-1-propane sulfonate (NDSB-201)
Resolution 2.90 Å R-free 0.242
9B9G Structure of the PI4KA complex bound to Calcineurin Deposited 2024-04-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain E 1–308（308 aa）
Chain G 1–308（308 aa）
Not recorded CA CALCIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；Freshly prepared gel filtration buffer, filtered through 0.22um filter and degassed
cryo-EM vitrification conditions Cryogen ETHANE；Blot force -5, blot time 1 s
Resolution 3.50 Å
9BAX PI4KA complex bound to C-terminus of EFR3A Deposited 2024-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–308（308 aa）
Chain G 1–308（308 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7；Freshly prepared gel filtration buffer, filtered through 0.22um filter and degassed
cryo-EM vitrification conditions Cryogen ETHANE；Blot force -5, blot time 1.5 s
Resolution 3.65 Å
9OT6 Cryo-EM structure of the PI4KA complex bound to an EFR3 interfering nanobody (F3IN) Deposited 2025-05-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–308（308 aa） Fragment：residues 1-308
Chain G 1–308（308 aa） Fragment：residues 1-308
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE；Blot force -5, blot time 1.5 s.
Resolution 3.54 Å

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

View Construct and Data Evidence
UniProt name HYCCI_HUMAN
Isoform Q9BYI3-3
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 5–292； UniProt 2–289 Author chain G； PDBConstruct 5–292； UniProt 2–289

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 6bq1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6bq1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6bq1
Deposition date deposition_date2017-11-27
Structure title titleHuman PI4KIIIa lipid kinase complex
Keywords keywordskinase, phosphoinositide synthesis, Transferase-Signaling Protein complex; Transferase/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_guinier76.04 Å
Radius of gyration Rg (electron density) rg_electron76.65 Å
Forward intensity I(0) i03903340000.00
Molecular weight molecular_weight527500.0 kDa
Excluded volume excluded_volume659190 ų
Envelope volume envelope_volume1131800 ų
Hydration-shell volume shell_volume129640 ų
Envelope diameter envelope_diameter285.5 Å
Shell Rg shell_rg67.49 Å
Envelope Rg envelope_rg75.26 Å
Shape Rg shape_rg76.65 Å
Total Rg total_rg76.52 Å
Total atoms total_atoms37217
Residues n_residues5003
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 dmax255.5 Å
Rg (real space) rg_real76.29 Å
Rg uncertainty (real space) rg_real_error2.22 Å
I(0) (real space) i0_real3.9000e+09
I(0) uncertainty (real space) i0_real_error7.8780e+07
Rg (reciprocal space) rg_reciprocal74.39 Å
I(0) (reciprocal space) i0_reciprocal3886000000.0000
Solution quality estimate total_estimate0.8491
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary73.0 Å
Skewness Skewness skewness0.497
Kurtosis Kurtosis kurtosis-0.204
Angular range angular_range— – 0.1050 Å−1
Current regularization parameter α current_alpha0.0106
Highest regularization parameter α highest_alpha172900000.0000
Real-space data points n_real_points22
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.355
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)