4F99

Human CDC7 kinase in complex with DBF4 and nucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of human CDC7 kinase in complex with its activator DBF4.

Hughes, S.Elustondo, F.Di Fonzo, A.Leroux, F.G.Wong, A.C.Snijders, A.P.Matthews, S.J.Cherepanov, P.

(2012) Nat Struct Mol Biol 19: 1101-1107

  • DOI: 10.1038/nsmb.2404
  • Primary Citation of Related Structures:  
    4F9A, 4F9B, 4F9C, 4F99

  • PubMed Abstract: 
  • CDC7 is a serine/threonine kinase that is essential for the initiation of eukaryotic DNA replication. CDC7 activity is controlled by its activator, DBF4. Here we present crystal structures of human CDC7-DBF4 in complex with a nucleotide or ATP-compet ...

    CDC7 is a serine/threonine kinase that is essential for the initiation of eukaryotic DNA replication. CDC7 activity is controlled by its activator, DBF4. Here we present crystal structures of human CDC7-DBF4 in complex with a nucleotide or ATP-competing small molecules, revealing the active and inhibited forms of the kinase, respectively. DBF4 wraps around CDC7, burying approximately 6,000 Å(2) of hydrophobic molecular surface in a bipartite interface. The effector domain of DBF4, containing conserved motif C, is essential and sufficient to support CDC7 kinase activity by binding to the kinase N-terminal lobe and stabilizing its canonical αC helix. DBF4 motif M latches onto the C-terminal lobe of the kinase, acting as a tethering domain. Our results elucidate the structural basis for binding to and activation of CDC7 by DBF4 and provide a framework for the design of more potent and specific CDC7 inhibitors.


    Organizational Affiliation

    Cancer Research UK, London Research Institute, Clare Hall Laboratories, Potters Bar, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division cycle 7-related protein kinaseA361Homo sapiensMutation(s): 0 
Gene Names: CDC7CDC7L1
EC: 2.7.11.1
Find proteins for O00311 (Homo sapiens)
Explore O00311 
Go to UniProtKB:  O00311
NIH Common Fund Data Resources
PHAROS  O00311
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein DBF4 homolog AB144Homo sapiensMutation(s): 0 
Gene Names: ASKDBF4DBF4AZDBF1
Find proteins for Q9UBU7 (Homo sapiens)
Explore Q9UBU7 
Go to UniProtKB:  Q9UBU7
NIH Common Fund Data Resources
PHAROS  Q9UBU7
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
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.48α = 90
b = 61.48β = 90
c = 237.41γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
BALBESphasing
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2012-12-12
    Changes: Database references
  • Version 1.2: 2017-08-16
    Changes: Source and taxonomy
  • Version 1.3: 2017-11-15
    Changes: Refinement description