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- EMDB-53531: Cryo-EM structure of the complex CDK16:CCNY:14-3-3 -

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Basic information

Entry
Database: EMDB / ID: EMD-53531
TitleCryo-EM structure of the complex CDK16:CCNY:14-3-3
Map datafinal refined map, sharpened
Sample
  • Complex: CDK16:CCNY:14-3-3
    • Protein or peptide: 14-3-3 protein eta
    • Protein or peptide: Cyclin-dependent kinase 16
    • Protein or peptide: Cyclin-Y
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
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 / 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
Cyclin-dependent kinase 16 / 14-3-3 protein eta / Cyclin-Y
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKosek D / Kohoutova K / Obsilova V / Obsil T
Funding support Czech Republic, 1 items
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, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53531.png

Downloads & links

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Map

FileDownload / File: emd_53531.map.gz / Format: CCP4 / Size: 113.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfinal refined map, sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.83 Å/pix.
x 310 pix.
= 258.416 Å		0.83 Å/pix.
x 310 pix.
= 258.416 Å		0.83 Å/pix.
x 310 pix.
= 258.416 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8336 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5
Minimum - Maximum-47.5608 - 65.046469999999999
Average (Standard dev.)-0.00000000101209 (±1.0000004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions310310310
Spacing310310310
CellA=B=C: 258.416 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53531_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: final refined map

Fileemd_53531_additional_1.map
Annotationfinal refined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53531_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53531_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : CDK16:CCNY:14-3-3

EntireName: CDK16:CCNY:14-3-3
Components
  • Complex: CDK16:CCNY:14-3-3
    • Protein or peptide: 14-3-3 protein eta
    • Protein or peptide: Cyclin-dependent kinase 16
    • Protein or peptide: Cyclin-Y
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: CDK16:CCNY:14-3-3

SupramoleculeName: CDK16:CCNY:14-3-3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
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
Details: Expressed with N-terminal His-tag fusion, cleaved with TEV protease
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-dependent kinase 16

MacromoleculeName: Cyclin-dependent kinase 16 / type: protein_or_peptide / ID: 2
Details: Expressed as N-terminal GST fusion, cleaved with Precission protease
Number of copies: 1 / Enantiomer: LEVO / EC number: cyclin-dependent kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.088801 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPLGSRKIST EDINKRLSLP ADIRLPEGYL EKLTLNSPIF DKPLSRRLRR VSLSEIGFGK LETYIKLDKL GEGTYATVYK GKSKLTDNL VALKEIRLEH EEGAPCTAIR EVSLLKDLKH ANIVTLHDII HTEKSLTLVF EYLDKDLKQY LDDCGNIINM H NVKLFLFQ ...String:
GPLGSRKIST EDINKRLSLP ADIRLPEGYL EKLTLNSPIF DKPLSRRLRR VSLSEIGFGK LETYIKLDKL GEGTYATVYK GKSKLTDNL VALKEIRLEH EEGAPCTAIR EVSLLKDLKH ANIVTLHDII HTEKSLTLVF EYLDKDLKQY LDDCGNIINM H NVKLFLFQ LLRGLAYCHR QKVLHRDLKP QNLLINERGE LKLADFGLAR AKSIPTKTYS NEVVTLWYRP PDILLGSTDY ST QIDMWGV GCIFYEMATG RPLFPGSTVE EQLHFIFRIL GTPTEETWPG ILSNEEFKTY NYPKYRAEAL LSHAPRLDSD GAD LLTKLL QFEGRNRISA EDAMKHPFFL SLGERIHKLP DTTSIFALKE IQLQKEASLR SSSMPDSGRP AFRVVDTEF

UniProtKB: Cyclin-dependent kinase 16

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Macromolecule #3: Cyclin-Y

MacromoleculeName: Cyclin-Y / type: protein_or_peptide / ID: 3
Details: Expressed as N-terminal GST fusion, cleaved with Precission protease Stoichiometrically phosphorylated at S66, S100, S326 Mutations Y98R, S99A, S324A
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.004074 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPLGSMGNTT SCCVSSSPKL RRNAHSRLES YRPDTDLSRE DTGCNLQHIS DRENIDDLNM EFNPSDHPRA (SEP)TIFLS KSQ TDVREKRKSL FINHHPPGQI ARKRA(SEP)CSTI FLDDSTVSQP NLKYTIKCVA LAIYYHIKNR DPDGRMLLDI FDE NLHPLS ...String:
GPLGSMGNTT SCCVSSSPKL RRNAHSRLES YRPDTDLSRE DTGCNLQHIS DRENIDDLNM EFNPSDHPRA (SEP)TIFLS KSQ TDVREKRKSL FINHHPPGQI ARKRA(SEP)CSTI FLDDSTVSQP NLKYTIKCVA LAIYYHIKNR DPDGRMLLDI FDE NLHPLS KSEVPPDYDK HNPEQKQIYR FVRTLFSAAQ LTAECAIVTL VYLERLLTYA EIDICPANWK RIVLGAILLA SKVW DDQAV WNVDYCQILK DITVEDMNEL ERQFLELLQF NINVPSSVYA KYYFDLRSLA EANNLSFPLE PLSRERAHKL EAISR LCED KYKDLRRSAR KRAA(SEP)ADNLT LPRWSPAIIS

UniProtKB: Cyclin-Y

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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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

Concentration1.5 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 and supplemented with 2 mM ATP-gamma-S
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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 204710
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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