[English] 日本語
Yorodumi
- EMDB-53533: Cryo-EM structure of the complex CCNY:14-3-3 -

+
Open data


ID or keywords:

Loading...

-
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: 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

-
Structure visualization

Supplemental images

emd_53533.png

Downloads & links

-
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
Brightness
Contrast
Others
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)

Slices (2/3)

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 °

-
Supplemental data

-
Mask #1

Fileemd_53533_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: final refined map

Fileemd_53533_additional_1.map
Annotationfinal refined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_53533_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_53533_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more