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- PDB-9r2i: Cryo-EM structure of the complex CDK16:CCNY:14-3-3 -

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Basic information

Entry
Database: PDB / ID: 9r2i
TitleCryo-EM structure of the complex CDK16:CCNY:14-3-3
Components
  • 14-3-3 protein eta
  • Cyclin-Y
  • Cyclin-dependent kinase 16
KeywordsCYTOSOLIC PROTEIN / Kinase / Phosphorylation / Cell signalling / Cryo-EM
Function / homology
Function and homology information


cytoplasmic cyclin-dependent protein kinase holoenzyme complex / glucocorticoid catabolic process / cerebellar granule cell to Purkinje cell synapse / growth hormone secretion / regulation of cell cycle phase transition / nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of dendrite morphogenesis / nuclear glucocorticoid receptor binding / regulation of insulin secretion involved in cellular response to glucose stimulus / membrane depolarization during action potential ...cytoplasmic cyclin-dependent protein kinase holoenzyme complex / glucocorticoid catabolic process / cerebellar granule cell to Purkinje cell synapse / growth hormone secretion / regulation of cell cycle phase transition / nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of dendrite morphogenesis / nuclear glucocorticoid receptor binding / regulation of insulin secretion involved in cellular response to glucose stimulus / membrane depolarization during action potential / positive regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of canonical Wnt signaling pathway / regulation of neuron differentiation / cyclin-dependent protein serine/threonine kinase regulator activity / exocytosis / intercalated disc / sodium channel regulator activity / Activation of BAD and translocation to mitochondria / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cyclin-dependent protein kinase holoenzyme complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / regulation of sodium ion transport / insulin-like growth factor receptor binding / Transcriptional and post-translational regulation of MITF-M expression and activity / substantia nigra development / positive regulation of autophagy / presynaptic modulation of chemical synaptic transmission / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intracellular protein transport / regulation of synaptic plasticity / G2/M transition of mitotic cell cycle / cytoplasmic side of plasma membrane / Wnt signaling pathway / neuron projection development / synaptic vesicle / intracellular protein localization / presynapse / microtubule cytoskeleton / actin binding / spermatogenesis / protein phosphorylation / transmembrane transporter binding / neuron projection / protein heterodimerization activity / protein domain specific binding / cell division / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / positive regulation of DNA-templated transcription / nucleolus / enzyme binding / signal transduction / mitochondrion / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Cyclin Y / Cyclin, N-terminal / Cyclin, N-terminal domain / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily ...Cyclin Y / Cyclin, N-terminal / Cyclin, N-terminal domain / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Cyclin-dependent kinase 16 / 14-3-3 protein eta / Cyclin-Y
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKosek, D. / Kohoutova, K. / Obsilova, V. / Obsil, T.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation25-15222S Czech Republic
CitationJournal: Nature / Year: 2026
Title: 14-3-3 Binding Unmasks the CDK16-binding Surface of Cyclin Y
Authors: Kohoutova, K. / Tomas, O.
History
DepositionApr 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein eta
B: 14-3-3 protein eta
C: Cyclin-dependent kinase 16
D: Cyclin-Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,5346
Polymers141,9874
Non-polymers5482
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein 14-3-3 protein eta / Protein AS1


Mass: 28446.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Expressed with N-terminal His-tag fusion, cleaved with TEV protease
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAH, YWHA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04917
#2: Protein Cyclin-dependent kinase 16 / Cell division protein kinase 16 / PCTAIRE-motif protein kinase 1 / Serine/threonine-protein kinase PCTAIRE-1


Mass: 45088.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Expressed as N-terminal GST fusion, cleaved with Precission protease
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK16, PCTAIRE1, PCTK1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00536, cyclin-dependent kinase
#3: Protein Cyclin-Y / Cyc-Y / Cyclin box protein 1 / Cyclin fold protein 1 / cyclin-X


Mass: 40004.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Expressed as N-terminal GST fusion, cleaved with Precission protease Stoichiometrically phosphorylated at S66, S100, S326 Mutations Y98R, S99A, S324A
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNY, C10orf9, CBCP1, CFP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ND76
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CDK16:CCNY:14-3-3 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Details: 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
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 105000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.21rc1_5127model refinement
13cryoSPARC4.1.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 204710 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049310
ELECTRON MICROSCOPYf_angle_d0.46212586
ELECTRON MICROSCOPYf_dihedral_angle_d9.113551
ELECTRON MICROSCOPYf_chiral_restr0.0341405
ELECTRON MICROSCOPYf_plane_restr0.0031614

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