9b9g

Structure of the PI4KA complex bound to Calcineurin

Method: ELECTRON MICROSCOPY Dmax: 282.1 Å Quality: EXCELLENT

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

Phosphatidylinositol 4-kinase alpha

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 × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain A; UniProt 1–2102 Chain B; UniProt 1–2102 Not recorded Tetratricopeptide repeat protein 7B × 2 (Q86TV6) Hyccin × 2 (Q9BYI3) Calcineurin subunit B type 1 × 2 (P63098) Protein phosphatase 3 catalytic subunit alpha × 2 (Q08209) 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

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 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PI4KA_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–2102; UniProt 1–2102 Author chain B; PDBConstruct 1–2102; UniProt 1–2102

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 × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain D; UniProt 1–843 Chain F; UniProt 1–843 Not recorded Phosphatidylinositol 4-kinase alpha × 2 (P42356) Hyccin × 2 (Q9BYI3) Calcineurin subunit B type 1 × 2 (P63098) Protein phosphatase 3 catalytic subunit alpha × 2 (Q08209) 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

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.

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 D; PDBConstruct 1–843; UniProt 1–843 Author chain F; PDBConstruct 1–843; UniProt 1–843

Hyccin

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 × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain E; UniProt 1–308 Chain G; UniProt 1–308 Not recorded Phosphatidylinositol 4-kinase alpha × 2 (P42356) Tetratricopeptide repeat protein 7B × 2 (Q86TV6) Calcineurin subunit B type 1 × 2 (P63098) Protein phosphatase 3 catalytic subunit alpha × 2 (Q08209) 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

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.

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
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 1–308; UniProt 1–308 Author chain G; PDBConstruct 1–308; UniProt 1–308

Calcineurin subunit B type 1

Homo sapiens

UniProt P63098

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 × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain H; UniProt 1–170 Chain J; UniProt 1–170 Not recorded Phosphatidylinositol 4-kinase alpha × 2 (P42356) Tetratricopeptide repeat protein 7B × 2 (Q86TV6) Hyccin × 2 (Q9BYI3) Protein phosphatase 3 catalytic subunit alpha × 2 (Q08209) 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

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.

20 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CANB1_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain H; PDBConstruct 1–170; UniProt 1–170 Author chain J; PDBConstruct 1–170; UniProt 1–170

Protein phosphatase 3 catalytic subunit alpha

Homo sapiens

UniProt Q08209

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 × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain I; UniProt 2–391 Chain I; UniProt 162–391 Chain K; UniProt 2–391 Chain K; UniProt 162–391 Mutation:L236P,D238N Phosphatidylinositol 4-kinase alpha × 2 (P42356) Tetratricopeptide repeat protein 7B × 2 (Q86TV6) Hyccin × 2 (Q9BYI3) Calcineurin subunit B type 1 × 2 (P63098) 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

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.

20 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PP2BA_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain I; PDBConstruct 1–390; UniProt 2–391 Author chain I; PDBConstruct 391–620; UniProt 162–391 Author chain K; PDBConstruct 1–390; UniProt 2–391 Author chain K; PDBConstruct 391–620; UniProt 162–391

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 9b9g

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9b9g
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9b9g
Deposition date deposition_date2024-04-02
Structure title titleStructure of the PI4KA complex bound to Calcineurin
Keywords keywordsPI4KIIIa complex, PI4KA, TTC7B, FAM126A, CNA, CNB, Calcineurin, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier78.99
Radius of gyration Rg (electron density) rg_electron79.06
Forward intensity I(0) i06160680000.00
Molecular weight molecular_weight692110.0 kDa
Excluded volume excluded_volume876440 ų
Envelope volume envelope_volume1609800 ų
Hydration-shell volume shell_volume170750 ų
Envelope diameter envelope_diameter279.4
Shell Rg shell_rg76.78
Envelope Rg envelope_rg75.38
Shape Rg shape_rg79.06
Total Rg total_rg79.03
Total atoms total_atoms48664
Residues n_residues6075
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 dmax282.1
Rg (real space) rg_real83.23
Rg uncertainty (real space) rg_real_error1.96
I(0) (real space) i0_real6.1960e+09
I(0) uncertainty (real space) i0_real_error1.4240e+08
Rg (reciprocal space) rg_reciprocal78.88
I(0) (reciprocal space) i0_reciprocal6158000000.0000
Solution quality estimate total_estimate0.9026
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary84.6
Skewness Skewness skewness0.489
Kurtosis Kurtosis kurtosis-0.065
Angular range angular_range— – 0.1000 −1
Current regularization parameter α current_alpha1.1020
Highest regularization parameter α highest_alpha449800000.0000
Real-space data points n_real_points21
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.866; Stabil: 0.857; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.608

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)