5EFQ

Crystal structure of human Cdk13/Cyclin K in complex with ADP-aluminum fluoride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and Functional Analysis of the Cdk13/Cyclin K Complex.

Greifenberg, A.K.Honig, D.Pilarova, K.Duster, R.Bartholomeeusen, K.Bosken, C.A.Anand, K.Blazek, D.Geyer, M.

(2016) Cell Rep 14: 320-331

  • DOI: 10.1016/j.celrep.2015.12.025
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Cyclin-dependent kinases regulate the cell cycle and transcription in higher eukaryotes. We have determined the crystal structure of the transcription kinase Cdk13 and its Cyclin K subunit at 2.0 Å resolution. Cdk13 contains a C-terminal extension he ...

    Cyclin-dependent kinases regulate the cell cycle and transcription in higher eukaryotes. We have determined the crystal structure of the transcription kinase Cdk13 and its Cyclin K subunit at 2.0 Å resolution. Cdk13 contains a C-terminal extension helix composed of a polybasic cluster and a DCHEL motif that interacts with the bound ATP. Cdk13/CycK phosphorylates both Ser5 and Ser2 of the RNA polymerase II C-terminal domain (CTD) with a preference for Ser7 pre-phosphorylations at a C-terminal position. The peptidyl-prolyl isomerase Pin1 does not change the phosphorylation specificities of Cdk9, Cdk12, and Cdk13 but interacts with the phosphorylated CTD through its WW domain. Using recombinant proteins, we find that flavopiridol inhibits Cdk7 more potently than it does Cdk13. Gene expression changes after knockdown of Cdk13 or Cdk12 are markedly different, with enrichment of growth signaling pathways for Cdk13-dependent genes. Together, our results provide insights into the structure, function, and activity of human Cdk13/CycK.


    Organizational Affiliation

    Institute of Innate Immunity, Department of Structural Immunology, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany; Center of Advanced European Studies and Research, Group Physical Biochemistry, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany; Max Planck Institute of Molecular Physiology, Department of Physical Biochemistry, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany. Electronic address: geyer@uni-bonn.de.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 13A, C347Homo sapiensMutation(s): 0 
Gene Names: CDK13CDC2LCDC2L5CHEDKIAA1791
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
Find proteins for Q14004 (Homo sapiens)
Explore Q14004 
Go to UniProtKB:  Q14004
NIH Common Fund Data Resources
PHAROS  Q14004
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cyclin-KB, D268Homo sapiensMutation(s): 0 
Gene Names: CCNKCPR4
Find proteins for O75909 (Homo sapiens)
Explore O75909 
Go to UniProtKB:  O75909
NIH Common Fund Data Resources
PHAROS  O75909
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A, C
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
AF3
Query on AF3

Download CCD File 
A, C
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A,CL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.78α = 74.08
b = 81.82β = 84.26
c = 93.14γ = 76.89
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-01-20
    Changes: Database references
  • Version 1.2: 2016-01-27
    Changes: Database references