Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.94 kDa 
• Atom Count: 5164 
• Modelled Residue Count: 568 
• Deposited Residue Count: 581 
• Unique protein chains: 2

1W98

The structural basis of CDK2 activation by cyclin E

• PDB DOI: 10.2210/pdb1W98/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-10-07 Released: 2005-02-02 
• Deposition Author(s): Lowe, E.D., Honda, R., Dubinina, E., Skamnaki, V., Cook, A., Johnson, L.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.246 
• R-Value Work: 0.181 
• R-Value Observed: 0.185 

Literature

The Structure of Cyclin E1/Cdk2: Implications for Cdk2 Activation and Cdk2-Independent Roles

Honda, R., Lowe, E.D., Dubinina, E., Skamnaki, V., Cook, A., Brown, N., Johnson, L.N.

(2005) EMBO J 24: 452

• PubMed: 15660127 
• DOI: 10.1038/sj.emboj.7600554
• Primary Citation of Related Structures:  
  1W98


• PubMed Abstract: 
  

Cyclin E, an activator of phospho-CDK2 (pCDK2), is important for cell cycle progression in metazoans and is frequently overexpressed in cancer cells. It is essential for entry to the cell cycle from G0 quiescent phase, for the assembly of prereplication complexes and for endoreduplication in megakaryotes and giant trophoblast cells. We report the crystal structure of pCDK2 in complex with a truncated cyclin E1 (residues 81-363) at 2.25 A resolution. The N-terminal cyclin box fold of cyclin E1 is similar to that of cyclin A and promotes identical changes in pCDK2 that lead to kinase activation. The C-terminal cyclin box fold shows significant differences from cyclin A. It makes additional interactions with pCDK2, especially in the region of the activation segment, and contributes to CDK2-independent binding sites of cyclin E. Kinetic analysis with model peptide substrates show a 1.6-fold increase in kcat for pCDK2/cyclin E1 (81-363) over kcat of pCDK2/cyclin E (full length) and pCDK2/cyclin A. The structural and kinetic results indicate no inherent substrate discrimination between pCDK2/cyclin E and pCDK2/cyclin A with model substrates.

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Organizational Affiliation: 

Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELL DIVISION PROTEIN KINASE 2	A	298	Homo sapiens	Mutation(s): 0  Gene Names: CDK2, CDKN2 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens) Explore P24941  Go to UniProtKB:  P24941
PHAROS:  P24941 GTEx:  ENSG00000123374

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
G1/S-SPECIFIC CYCLIN E1	B	283	Homo sapiens	Mutation(s): 0  Gene Names: CCNE1, CCNE
UniProt & NIH Common Fund Data Resources
Find proteins for P24864 (Homo sapiens) Explore P24864  Go to UniProtKB:  P24864
PHAROS:  P24864 GTEx:  ENSG00000105173

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.246 
• R-Value Work: 0.181 
• R-Value Observed: 0.185 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.62	α = 90
b = 99.62	β = 90
c = 149.987	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-10-07 
• Released Date: 2005-02-02 
Deposition Author(s): Lowe, E.D., Honda, R., Dubinina, E., Skamnaki, V., Cook, A., Johnson, L.N.

Revision History  

• Version 1.0: 2005-02-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance