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- PDB-9r2n: Cryo-EM structure of the complex CCNY:14-3-3 -

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Basic information

Entry
Database: PDB / ID: 9r2n
TitleCryo-EM structure of the complex CCNY:14-3-3
Components
  • 14-3-3 protein eta
  • Cyclin-Y
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 / nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of dendrite morphogenesis / nuclear glucocorticoid receptor binding / 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 ...cytoplasmic cyclin-dependent protein kinase holoenzyme complex / glucocorticoid catabolic process / cerebellar granule cell to Purkinje cell synapse / nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of dendrite morphogenesis / nuclear glucocorticoid receptor binding / 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 / intercalated disc / sodium channel regulator activity / Activation of BAD and translocation to mitochondria / 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 / Wnt signaling pathway / intracellular protein localization / presynapse / actin binding / spermatogenesis / transmembrane transporter binding / protein heterodimerization activity / protein domain specific binding / cell division / protein kinase binding / positive regulation of DNA-templated transcription / nucleolus / enzyme binding / signal transduction / mitochondrion / extracellular exosome / nucleoplasm / 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
Similarity search - Domain/homology
14-3-3 protein eta / Cyclin-Y
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.83 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
D: Cyclin-Y


Theoretical massNumber of molelcules
Total (without water)96,8183
Polymers96,8183
Non-polymers00
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
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAH, YWHA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04917
#2: Protein Cyclin-Y / Cyc-Y / Cyclin box protein 1 / Cyclin fold protein 1 / cyclin-X


Mass: 39924.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Mutant Y98R, S99A, S324A / Source: (gene. exp.) Homo sapiens (human) / Gene: CCNY, C10orf9, CBCP1, CFP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ND76
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: CCNY:14-3-3 / Type: COMPLEX / Entity ID: all / 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
SpecimenConc.: 1.3 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: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91774 / Symmetry type: POINT
RefinementHighest resolution: 3.83 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025934
ELECTRON MICROSCOPYf_angle_d0.3898014
ELECTRON MICROSCOPYf_dihedral_angle_d9.6012270
ELECTRON MICROSCOPYf_chiral_restr0.029890
ELECTRON MICROSCOPYf_plane_restr0.0021035

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