Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 65.61 kDa 
• Atom Count: 4036 
• Residue Count: 498 
• Unique protein chains: 2

2W9F

Crystal Structure of CDK4 in complex with a D-type cyclin

• DOI: 10.2210/pdb2W9F/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2009-01-23 Released: 2009-03-10 
• Deposition Author(s): Day, P.J., Cleasby, A., Tickle, I.J., Reilly, M.O., Coyle, J.E., Holding, F.P., McMenamin, R.L., Yon, J., Chopra, R., Lengauer, C., Jhoti, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.300 
• R-Value Work: 0.225 
• R-Value Observed: 0.229 

Literature

Crystal Structure of Human Cdk4 in Complex with a D-Type Cyclin.

Day, P.J., Cleasby, A., Tickle, I.J., O'Reilly, M., Coyle, J.E., Holding, F.P., Mcmenamin, R.L., Yon, J., Chopra, R., Lengauer, C., Jhoti, H.

(2009) Proc Natl Acad Sci U S A 106: 4166

• PubMed: 19237565 
• DOI: 10.1073/pnas.0809645106
• Primary Citation of Related Structures:  
  2W9F, 2W96, 2W99, 2W9Z


• PubMed Abstract: 
  

The cyclin D1-cyclin-dependent kinase 4 (CDK4) complex is a key regulator of the transition through the G(1) phase of the cell cycle. Among the cyclin/CDKs, CDK4 and cyclin D1 are the most frequently activated by somatic genetic alterations in multiple tumor types. Thus, aberrant regulation of the CDK4/cyclin D1 pathway plays an essential role in oncogenesis; hence, CDK4 is a genetically validated therapeutic target. Although X-ray crystallographic structures have been determined for various CDK/cyclin complexes, CDK4/cyclin D1 has remained highly refractory to structure determination. Here, we report the crystal structure of CDK4 in complex with cyclin D1 at a resolution of 2.3 A. Although CDK4 is bound to cyclin D1 and has a phosphorylated T-loop, CDK4 is in an inactive conformation and the conformation of the heterodimer diverges from the previously known CDK/cyclin binary complexes, which suggests a unique mechanism for the process of CDK4 regulation and activation.

---

Organizational Affiliation: 

Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
G1/S-SPECIFIC CYCLIN-D1	A	271	Homo sapiens	Mutation(s): 0  Gene Names: CCND1, BCL1, PRAD1
Find proteins for P24385 (Homo sapiens) Explore P24385  Go to UniProtKB:  P24385
NIH Common Fund Data Resources
PHAROS  P24385 GTEx  ENSG00000110092

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CELL DIVISION PROTEIN KINASE 4	B	306	Homo sapiens	Mutation(s): 3  Gene Names: CDK4 EC: 2.7.11.22
Find proteins for P11802 (Homo sapiens) Explore P11802  Go to UniProtKB:  P11802
NIH Common Fund Data Resources
PHAROS  P11802 GTEx  ENSG00000135446

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.300 
• R-Value Work: 0.225 
• R-Value Observed: 0.229 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58	α = 90
b = 64.277	β = 90
c = 187.617	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-01-23 
• Released Date: 2009-03-10 
Deposition Author(s): Day, P.J., Cleasby, A., Tickle, I.J., Reilly, M.O., Coyle, J.E., Holding, F.P., McMenamin, R.L., Yon, J., Chopra, R., Lengauer, C., Jhoti, H.

Revision History 

• Version 1.0: 2009-03-10
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-04-24
  Changes: Data collection, Other, Source and taxonomy