← Back to search
5dse

Crystal Structure of the TTC7B/Hyccin Complex

Method: X-RAY DIFFRACTION Dmax: 144.6 Å Quality: EXCELLENT
▼

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

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 7–843 Not recorded Hyccin × 1 （Q9BYI3） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 7–843 Not recorded Hyccin × 1 （Q9BYI3） 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

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 5DSE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6BQ1 Human PI4KIIIa lipid kinase complex Deposited 2017-11-27 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 × 6 PDB declaration: hexameric
Chain B 1–843（843 aa）
Chain F 1–843（843 aa）
Not recorded 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
9B9G Structure of the PI4KA complex bound to Calcineurin Deposited 2024-04-02 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 × 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TTC7B_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–837； UniProt 7–843 Author chain C； PDBConstruct 1–837； UniProt 7–843

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 2–308 Not recorded Tetratricopeptide repeat protein 7B × 1 （Q86TV6） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 2–308 Not recorded Tetratricopeptide repeat protein 7B × 1 （Q86TV6） 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

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 5DSE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6BQ1 Human PI4KIIIa lipid kinase complex Deposited 2017-11-27 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 × 6 PDB declaration: hexameric
Chain C 2–289（288 aa）
Chain G 2–289（288 aa）
Not recorded 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
9B9G Structure of the PI4KA complex bound to Calcineurin Deposited 2024-04-02 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 × 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HYCCI_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 6–312； UniProt 2–308 Author chain D； PDBConstruct 6–312； UniProt 2–308

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 5dse

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5dse
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id5dse
Deposition date deposition_date2015-09-17
Structure title titleCrystal Structure of the TTC7B/Hyccin Complex
Keywords keywordsPI4P synthesis, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier44.50 Å
Radius of gyration Rg (electron density) rg_electron43.95 Å
Forward intensity I(0) i0535547000.00
Molecular weight molecular_weight196580.0 kDa
Excluded volume excluded_volume248590 ų
Envelope volume envelope_volume345260 ų
Hydration-shell volume shell_volume65075 ų
Envelope diameter envelope_diameter144.8 Å
Shell Rg shell_rg49.51 Å
Envelope Rg envelope_rg42.93 Å
Shape Rg shape_rg43.95 Å
Total Rg total_rg44.21 Å
Total atoms total_atoms13824
Residues n_residues1744
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax144.6 Å
Rg (real space) rg_real44.42 Å
Rg uncertainty (real space) rg_real_error1.30 Å
I(0) (real space) i0_real5.3550e+08
I(0) uncertainty (real space) i0_real_error9.2540e+06
Rg (reciprocal space) rg_reciprocal44.50 Å
I(0) (reciprocal space) i0_reciprocal535600000.0000
Solution quality estimate total_estimate0.9013
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary53.7 Å
Skewness Skewness skewness0.187
Kurtosis Kurtosis kurtosis-0.628
Angular range angular_range— – 0.1750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha46270000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.890
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▶

8. Citations (1)

▶

9. Files and Curves (10)