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- EMDB-53533: Cryo-EM structure of the complex CCNY:14-3-3 -

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Basic information

Entry
Database: EMDB / ID: EMD-53533
TitleCryo-EM structure of the complex CCNY:14-3-3
Map datafinal refined map, sharpened
Sample
  • Complex: CCNY:14-3-3
    • Protein or peptide: 14-3-3 protein eta
    • Protein or peptide: Cyclin-Y
KeywordsKinase / Phosphorylation / Cell signalling / Cryo-EM / CYTOSOLIC PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsKosek D / Kohoutova K / Obsilova V / Obsil T
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Czech Science Foundation25-15222S Czech Republic
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis of the cyclin Y/14-3-3 protein-mediated activation of CDK16.
Authors: Klara Kohoutova / Dalibor Kosek / Adam Brzezina / Karolina Honzejkova / Veronika Obsilova / Tomas Obsil /
Abstract: Cyclin-dependent protein kinase 16 (CDK16) regulates both physiological and pathological processes, including autophagy, spermatogenesis and cancer. Unlike other CDKs, CDK16 is regulated by an ...Cyclin-dependent protein kinase 16 (CDK16) regulates both physiological and pathological processes, including autophagy, spermatogenesis and cancer. Unlike other CDKs, CDK16 is regulated by an unclear mechanism involving phosphorylated cyclin Y (CCNY) in complex with 14-3-3 proteins rather than CCNY alone. The present study aims at elucidating this mechanism by structurally characterizing CDK16 in complex with CCNY and 14-3-3 using several biophysical techniques. As shown by cryo-EM analysis and hydrogen/deuterium exchange coupled to mass spectrometry, 14-3-3 binding modulates the conformation of a key moiety of the CDK binding surface of CCNY, thereby enabling CDK16 activation. CDK16 interacts with the cyclin box of CCNY, while 14-3-3 provides additional contacts, including with the activation segment of CDK16. CDK16 activation also requires interactions of CCNY with the N-terminal extension of CDK16. These findings not only clarify the role of CCNY and 14-3-3 in CDK16 activation but also highlight the potential of targeting CDK16 protein-protein interactions for cancer therapy.
History
DepositionApr 30, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53533.png

Downloads & links

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Map

FileDownload / File: emd_53533.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfinal refined map, sharpened
Projections & slices

Image control

Size
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AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 320 pix.
= 266.752 Å		0.83 Å/pix.
x 320 pix.
= 266.752 Å		0.83 Å/pix.
x 320 pix.
= 266.752 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8336 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-27.269010000000002 - 40.609699999999997
Average (Standard dev.)0.000000000003054 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.75198 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53533_msk_1.map
Projections & Slices
AxesZYX

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Additional map: final refined map

Fileemd_53533_additional_1.map
Annotationfinal refined map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_53533_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_53533_half_map_2.map
Projections & Slices
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Sample components

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Entire : CCNY:14-3-3

EntireName: CCNY:14-3-3
Components
  • Complex: CCNY:14-3-3
    • Protein or peptide: 14-3-3 protein eta
    • Protein or peptide: Cyclin-Y

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Supramolecule #1: CCNY:14-3-3

SupramoleculeName: CCNY:14-3-3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 14-3-3 protein eta

MacromoleculeName: 14-3-3 protein eta / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.446918 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GHMGDREQLL QRARLAEQAE RYDDMASAMK AVTELNEPLS NEDRNLLSVA YKNVVGARRS SWRVISSIEQ KTMADGNEKK LEKVKAYRE KIEKELETVC NDVLSLLDKF LIKNCNDFQY ESKVFYLKMK GDYYRYLAEV ASGEKKNSVV EASEAAYKEA F EISKEQMQ ...String:
GHMGDREQLL QRARLAEQAE RYDDMASAMK AVTELNEPLS NEDRNLLSVA YKNVVGARRS SWRVISSIEQ KTMADGNEKK LEKVKAYRE KIEKELETVC NDVLSLLDKF LIKNCNDFQY ESKVFYLKMK GDYYRYLAEV ASGEKKNSVV EASEAAYKEA F EISKEQMQ PTHPIRLGLA LNFSVFYYEI QNAPEQACLL AKQAFDDAIA ELDTLNEDSY KDSTLIMQLL RDNLTLWTSD QQ DEEAGEG N

UniProtKB: 14-3-3 protein eta

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Macromolecule #2: Cyclin-Y

MacromoleculeName: Cyclin-Y / type: protein_or_peptide / ID: 2 / Details: Mutant Y98R, S99A, S324A / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.924098 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPLGSMGNTT SCCVSSSPKL RRNAHSRLES YRPDTDLSRE DTGCNLQHIS DRENIDDLNM EFNPSDHPRA STIFLSKSQT DVREKRKSL FINHHPPGQI ARKRA(SEP)CSTI FLDDSTVSQP NLKYTIKCVA LAIYYHIKNR DPDGRMLLDI FDENLHP LS KSEVPPDYDK ...String:
GPLGSMGNTT SCCVSSSPKL RRNAHSRLES YRPDTDLSRE DTGCNLQHIS DRENIDDLNM EFNPSDHPRA STIFLSKSQT DVREKRKSL FINHHPPGQI ARKRA(SEP)CSTI FLDDSTVSQP NLKYTIKCVA LAIYYHIKNR DPDGRMLLDI FDENLHP LS KSEVPPDYDK HNPEQKQIYR FVRTLFSAAQ LTAECAIVTL VYLERLLTYA EIDICPANWK RIVLGAILLA SKVWDDQA V WNVDYCQILK DITVEDMNEL ERQFLELLQF NINVPSSVYA KYYFDLRSLA EANNLSFPLE PLSRERAHKL EAISRLCED KYKDLRRSAR KRAA(SEP)ADNLT LPRWSPAIIS

UniProtKB: Cyclin-Y

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.3 mg/mL
BufferpH: 8
Details: 20 mM HEPES buffer (pH 8.0), 150 mM NaCl, 4 mM MgCl2, 0.5 mM TCEP and 7.8 mM CHAPSO
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 91774
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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