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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
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

Projections

Slices (1/2)
Density Histograms

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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