3RGF

Crystal Structure of human CDK8/CycC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Structure of CDK8/CycC Implicates Specificity in the CDK/Cyclin Family and Reveals Interaction with a Deep Pocket Binder.

Schneider, E.V.Bottcher, J.Blaesse, M.Neumann, L.Huber, R.Maskos, K.

(2011) J.Mol.Biol. 412: 251-266

  • DOI: 10.1016/j.jmb.2011.07.020

  • PubMed Abstract: 
  • Cyclin-dependent kinase (CDK) 8 associates with cyclin C (CycC) and belongs to the CDK module of the Mediator of transcription, together with MED12 and MED13. CDK8 is involved in the regulation of mRNA transcription and was identified as a potent onc ...

    Cyclin-dependent kinase (CDK) 8 associates with cyclin C (CycC) and belongs to the CDK module of the Mediator of transcription, together with MED12 and MED13. CDK8 is involved in the regulation of mRNA transcription and was identified as a potent oncogene in colon cancerogenesis. We have solved the 2.2-Å crystal structure of CDK8/CycC in complex with sorafenib, an anti-cancer drug of clinical relevance. The CDK8 structure reveals a unique CycC recognition helix that explains the specificity of the CDK8/CycC pair and discrimination among the highly promiscuous binding in the CDK/cyclin family. In contrast to all CDKs, the CDK8 activation loop appears not to be phosphorylated. Based on the structure, we discuss an alternate mode of CDK8 activation to the general CDK activation by T-loop phosphorylation. Sorafenib binds to the catalytic cleft of CDK8. It displays a deep pocket binding mode and is the first small molecule to induce a DFG-out conformation in the CDK family, which is actually DMG-out in CDK8.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Am Klopferspitz 18, D-82152 Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 8
A
405Homo sapiensMutation(s): 0 
Gene Names: CDK8
EC: 2.7.11.22, 2.7.11.23
Find proteins for P49336 (Homo sapiens)
Go to Gene View: CDK8
Go to UniProtKB:  P49336
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cyclin-C
B
285Homo sapiensMutation(s): 0 
Gene Names: CCNC
Find proteins for P24863 (Homo sapiens)
Go to Gene View: CCNC
Go to UniProtKB:  P24863
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
BAX
Query on BAX

Download SDF File 
Download CCD File 
A
4-{4-[({[4-CHLORO-3-(TRIFLUOROMETHYL)PHENYL]AMINO}CARBONYL)AMINO]PHENOXY}-N-METHYLPYRIDINE-2-CARBOXAMIDE
Sorafenib
C21 H16 Cl F3 N4 O3
MLDQJTXFUGDVEO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BAXKd: 250 - 310000 nM (91) BINDINGDB
BAXIC50: 130 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.690α = 90.00
b = 70.610β = 108.31
c = 79.140γ = 90.00
Software Package:
Software NamePurpose
BALBESphasing
SCALAdata scaling
RemDAqdata collection
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2011-09-07
    Type: Database references
  • Version 1.2: 2012-10-03
    Type: Non-polymer description