← Back to search
9r2i

Cryo-EM structure of the complex CDK16:CCNY:14-3-3

Method: ELECTRON MICROSCOPY Dmax: 122.8 Å Quality: GOOD
▼

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

14-3-3 protein eta

Homo sapiens

UniProt Q04917

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 1–246 Chain B； UniProt 1–246 Not recorded Cyclin-dependent kinase 16 × 1 （Q00536） Cyclin-Y × 1 （Q8ND76） MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8；20 mM HEPES buffer (pH 8.0), 150 mM NaCl, 4 mM MgCl2, 0.5 mM TCEP and 7.8 mM CHAPSO and supplemented with 2 mM ATP-gamma-S cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 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 9R2I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2C63 14-3-3 Protein Eta (Human) Complexed to Peptide Deposited 2005-11-07 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–245（245 aa）
Chain B 1–245（245 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.2M MGCL2, 0.1M HEPES PH 7.5, 25% PEG 3350
Resolution 2.15 Å R-free 0.248
2C63 14-3-3 Protein Eta (Human) Complexed to Peptide Deposited 2005-11-07 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–245（245 aa）
Chain D 1–245（245 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.2M MGCL2, 0.1M HEPES PH 7.5, 25% PEG 3350
Resolution 2.15 Å R-free 0.248
2C74 14-3-3 Protein Eta (Human) Complexed to Peptide Deposited 2005-11-17 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–245（245 aa）
Chain B 1–245（245 aa）
Not recorded CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；0.1M CITRATE PH 5.6, 20% ISOPROPANOL, 20% PEG4000
Resolution 2.70 Å R-free 0.291
7NMZ Structure of 14-3-3 eta in complex with Nedd4-2(335-455) containing two 14-3-3 binding motifs Ser342 and Ser448 Deposited 2021-02-23 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 × 3 PDB declaration: trimeric
Chain AA 1–234（234 aa）
Chain BA 1–234（234 aa）
Mutation：S235Stop Mutation：S235Stop No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03M of each NPS (sodium nitrate, sodium phosphate dibasic, ammonium sulfate), 0.1Mbicine/Trizma base pH 8.5, 30% sacharose
Resolution 2.30 Å R-free 0.235
9R2N Cryo-EM structure of the complex CCNY:14-3-3 Deposited 2025-04-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–246（246 aa）
Chain B 1–246（246 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPES buffer (pH 8.0), 150 mM NaCl, 4 mM MgCl2, 0.5 mM TCEP and 7.8 mM CHAPSO
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.83 Å

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

View Construct and Data Evidence
UniProt name 1433F_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–248； UniProt 1–246 Author chain B； PDBConstruct 3–248； UniProt 1–246

Cyclin-dependent kinase 16

Homo sapiens

UniProt Q00536

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 C； UniProt 107–496 Not recorded 14-3-3 protein eta × 2 （Q04917） Cyclin-Y × 1 （Q8ND76） MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8；20 mM HEPES buffer (pH 8.0), 150 mM NaCl, 4 mM MgCl2, 0.5 mM TCEP and 7.8 mM CHAPSO and supplemented with 2 mM ATP-gamma-S cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 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 9R2I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3MTL Crystal structure of the PCTAIRE1 kinase in complex with Indirubin E804 Deposited 2010-04-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 163–478（316 aa） Fragment：residues in UNP 163-478
Mutation：S319D FEF (2Z,3E)-2,3'-BIINDOLE-2',3(1H,1'H)-DIONE 3-{O-[(3R)-3,4-DIHYDROXYBUTYL]OXIME} × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；2.1M Na-formate, 0.1M Bis-Tris, pH 7.0, VAPOR DIFFUSION, temperature 293K
Resolution 2.40 Å R-free 0.263
3MTL Crystal structure of the PCTAIRE1 kinase in complex with Indirubin E804 Deposited 2010-04-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 163–478（316 aa） Fragment：residues in UNP 163-478
Mutation：S319D FEF (2Z,3E)-2,3'-BIINDOLE-2',3(1H,1'H)-DIONE 3-{O-[(3R)-3,4-DIHYDROXYBUTYL]OXIME} × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；2.1M Na-formate, 0.1M Bis-Tris, pH 7.0, VAPOR DIFFUSION, temperature 293K
Resolution 2.40 Å R-free 0.263
5G6V Crystal structure of the PCTAIRE1 kinase in complex with inhibitor Deposited 2016-08-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 163–478（316 aa） Fragment：KINASE DOMAIN, RESIDUES 163-478
Mutation：YES 919 4-[4-({[3-tert-butyl-1-(quinolin-6-yl)-1H-pyrazol-5-yl]carbamoyl}amino)-3-fluorophenoxy]-N-methylpyridine-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；25% PEG MEDIUM SMEAR (PEG 2000, PEG 3350, PEG 4000, PEG 5000MME) AND 0.1 M CITRATE PH 5.5
Resolution 2.20 Å R-free 0.271
5G6V Crystal structure of the PCTAIRE1 kinase in complex with inhibitor Deposited 2016-08-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 163–478（316 aa） Fragment：KINASE DOMAIN, RESIDUES 163-478
Mutation：YES 919 4-[4-({[3-tert-butyl-1-(quinolin-6-yl)-1H-pyrazol-5-yl]carbamoyl}amino)-3-fluorophenoxy]-N-methylpyridine-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；25% PEG MEDIUM SMEAR (PEG 2000, PEG 3350, PEG 4000, PEG 5000MME) AND 0.1 M CITRATE PH 5.5
Resolution 2.20 Å R-free 0.271

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

View Construct and Data Evidence
UniProt name CDK16_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 6–395； UniProt 107–496

Cyclin-Y

Homo sapiens

UniProt Q8ND76

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 D； UniProt 1–341 Non-standard monomer：Yes (specific site not provided by mmCIF) 14-3-3 protein eta × 2 （Q04917） Cyclin-dependent kinase 16 × 1 （Q00536） MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8；20 mM HEPES buffer (pH 8.0), 150 mM NaCl, 4 mM MgCl2, 0.5 mM TCEP and 7.8 mM CHAPSO and supplemented with 2 mM ATP-gamma-S cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 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 9R2I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9R2N Cryo-EM structure of the complex CCNY:14-3-3 Deposited 2025-04-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–341（341 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPES buffer (pH 8.0), 150 mM NaCl, 4 mM MgCl2, 0.5 mM TCEP and 7.8 mM CHAPSO
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.83 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CCNY_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 6–346； UniProt 1–341

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 9r2i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9r2i
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id9r2i
Deposition date deposition_date2025-04-30
Structure title titleCryo-EM structure of the complex CDK16:CCNY:14-3-3
Keywords keywordsKinase, Phosphorylation, Cell signalling, Cryo-EM, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
Experimental Method methodELECTRON MICROSCOPY
▼

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

Radius of gyration Rg (Guinier) rg_guinier37.18 Å
Radius of gyration Rg (electron density) rg_electron36.77 Å
Forward intensity I(0) i0258938000.00
Molecular weight molecular_weight130090.0 kDa
Excluded volume excluded_volume162920 ų
Envelope volume envelope_volume219390 ų
Hydration-shell volume shell_volume49691 ų
Envelope diameter envelope_diameter125.6 Å
Shell Rg shell_rg43.05 Å
Envelope Rg envelope_rg36.13 Å
Shape Rg shape_rg36.76 Å
Total Rg total_rg37.20 Å
Total atoms total_atoms18260
Residues n_residues1122
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 dmax122.8 Å
Rg (real space) rg_real37.15 Å
Rg uncertainty (real space) rg_real_error0.95 Å
I(0) (real space) i0_real2.5890e+08
I(0) uncertainty (real space) i0_real_error4.3560e+06
Rg (reciprocal space) rg_reciprocal37.17 Å
I(0) (reciprocal space) i0_reciprocal258900000.0000
Solution quality estimate total_estimate0.8912
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.7 Å
Skewness Skewness skewness0.283
Kurtosis Kurtosis kurtosis-0.450
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha58910000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.890
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

▶

8. Citations (1)

▶

9. Files and Curves (10)