9R2I | pdb_00009r2i

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9R2I

This is version 1.1 of the entry. See complete history

Literature

Structural basis of the cyclin Y/14-3-3 protein-mediated activation of CDK16.

Kohoutova, K.Kosek, D.Brzezina, A.Honzejkova, K.Obsilova, V.Obsil, T.

(2026) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-026-70778-5
  • Primary Citation Related Structures: 
    9R2I, 9R2N

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 142.53 kDa 
  • Atom Count: 9,145 
  • Modeled Residue Count: 1,125 
  • Deposited Residue Count: 1,237 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
14-3-3 protein eta
A, B
248Homo sapiensMutation(s): 0 
Gene Names: YWHAHYWHA1
UniProt & NIH Common Fund Data Resources
Find proteins for Q04917 (Homo sapiens)
Explore Q04917 
Go to UniProtKB:  Q04917
PHAROS:  Q04917
GTEx:  ENSG00000128245 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04917
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 16395Homo sapiensMutation(s): 0 
Gene Names: CDK16PCTAIRE1PCTK1
EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q00536 (Homo sapiens)
Explore Q00536 
Go to UniProtKB:  Q00536
PHAROS:  Q00536
GTEx:  ENSG00000102225 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00536
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cyclin-Y346Homo sapiensMutation(s): 3 
Gene Names: CCNYC10orf9CBCP1CFP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8ND76 (Homo sapiens)
Explore Q8ND76 
Go to UniProtKB:  Q8ND76
PHAROS:  Q8ND76
GTEx:  ENSG00000108100 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ND76
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
D
L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_5127
RECONSTRUCTIONcryoSPARC4.1.2

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Science FoundationCzech Republic25-15222S

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-25
    Type: Initial release
  • Version 1.1: 2026-04-01
    Changes: Data collection, Database references