4md7

Crystal Structure of full-length symmetric CK2 holoenzyme

Method: X-RAY DIFFRACTION Dmax: 182.1 Å Quality: GOOD

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

Casein kinase II subunit beta

Homo sapiens

UniProt P67870

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–215 Chain B; UniProt 1–215 Not recorded Casein kinase II subunit alpha × 2 (P68400) ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;277 K;20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K Resolution 3.10 Å R-free 0.263
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 1–215 Chain D; UniProt 1–215 Not recorded Casein kinase II subunit alpha × 2 (P68400) ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;277 K;20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K Resolution 3.10 Å R-free 0.263

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.

8 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CSK2B_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–215; UniProt 1–215 Author chain B; PDBConstruct 1–215; UniProt 1–215 Author chain C; PDBConstruct 1–215; UniProt 1–215 Author chain D; PDBConstruct 1–215; UniProt 1–215

Casein kinase II subunit alpha

Homo sapiens

UniProt P68400

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 1–391 Chain F; UniProt 1–391 Mutation:T344E/T360E/S362E/S370E Casein kinase II subunit beta × 2 (P67870) ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;277 K;20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K Resolution 3.10 Å R-free 0.263
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain G; UniProt 1–391 Chain H; UniProt 1–391 Mutation:T344E/T360E/S362E/S370E Casein kinase II subunit beta × 2 (P67870) ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;277 K;20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K Resolution 3.10 Å R-free 0.263

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.

313 other PDB entries and 447 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CSK21_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain E; PDBConstruct 1–391; UniProt 1–391 Author chain F; PDBConstruct 1–391; UniProt 1–391 Author chain G; PDBConstruct 1–391; UniProt 1–391 Author chain H; PDBConstruct 1–391; UniProt 1–391

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 4md7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4md7
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id4md7
Deposition date deposition_date2013-08-22
Structure title titleCrystal Structure of full-length symmetric CK2 holoenzyme
Keywords keywordsprotein serine/threonine kinase, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier53.39
Radius of gyration Rg (electron density) rg_electron53.11
Forward intensity I(0) i0886505000.00
Molecular weight molecular_weight249910.0 kDa
Excluded volume excluded_volume312700 ų
Envelope volume envelope_volume455870 ų
Hydration-shell volume shell_volume71729 ų
Envelope diameter envelope_diameter182.4
Shell Rg shell_rg56.63
Envelope Rg envelope_rg51.27
Shape Rg shape_rg53.17
Total Rg total_rg53.02
Total atoms total_atoms17621
Residues n_residues2112
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 dmax182.1
Rg (real space) rg_real53.45
Rg uncertainty (real space) rg_real_error1.96
I(0) (real space) i0_real8.8650e+08
I(0) uncertainty (real space) i0_real_error1.9380e+07
Rg (reciprocal space) rg_reciprocal53.32
I(0) (reciprocal space) i0_reciprocal886300000.0000
Solution quality estimate total_estimate0.8867
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary62.8
Skewness Skewness skewness0.280
Kurtosis Kurtosis kurtosis-0.529
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha45040000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.812

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd4md7a_
Class classg — Small proteins
Fold Fold foldg.41 — Rubredoxin-like
Superfamily Superfamily superfamilyg.41.4 — Casein kinase II beta subunit
Family Family familyg.41.4.1 — Casein kinase II beta subunit
Domain ID domain_idd4md7b_
Class classg — Small proteins
Fold Fold foldg.41 — Rubredoxin-like
Superfamily Superfamily superfamilyg.41.4 — Casein kinase II beta subunit
Family Family familyg.41.4.1 — Casein kinase II beta subunit
Domain ID domain_idd4md7c_
Class classg — Small proteins
Fold Fold foldg.41 — Rubredoxin-like
Superfamily Superfamily superfamilyg.41.4 — Casein kinase II beta subunit
Family Family familyg.41.4.1 — Casein kinase II beta subunit
Domain ID domain_idd4md7d_
Class classg — Small proteins
Fold Fold foldg.41 — Rubredoxin-like
Superfamily Superfamily superfamilyg.41.4 — Casein kinase II beta subunit
Family Family familyg.41.4.1 — Casein kinase II beta subunit
Domain ID domain_idd4md7e_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd4md7f_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd4md7g_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd4md7h_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (16 domains)

Domain ID domain_id4md7A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1820 — protein kinase ck2 holoenzyme, chain C, domain 1
Homologous superfamily homologous superfamily10 — protein kinase ck2 holoenzyme, chain C, domain 1
Domain ID domain_id4md7A02
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily20
Domain ID domain_id4md7B01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1820 — protein kinase ck2 holoenzyme, chain C, domain 1
Homologous superfamily homologous superfamily10 — protein kinase ck2 holoenzyme, chain C, domain 1
Domain ID domain_id4md7B02
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily20
Domain ID domain_id4md7C01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1820 — protein kinase ck2 holoenzyme, chain C, domain 1
Homologous superfamily homologous superfamily10 — protein kinase ck2 holoenzyme, chain C, domain 1
Domain ID domain_id4md7C02
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily20
Domain ID domain_id4md7D01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1820 — protein kinase ck2 holoenzyme, chain C, domain 1
Homologous superfamily homologous superfamily10 — protein kinase ck2 holoenzyme, chain C, domain 1
Domain ID domain_id4md7D02
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily20
Domain ID domain_id4md7E01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id4md7E02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id4md7F01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id4md7F02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id4md7G01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id4md7G02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id4md7H01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id4md7H02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1

8. Citations (1)

9. Files and Curves (10)