2AST

Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural Basis of the Cks1-Dependent Recognition of p27(Kip1) by the SCF(Skp2) Ubiquitin Ligase.

Hao, B., Zheng, N., Schulman, B.A., Wu, G., Miller, J.J., Pagano, M., Pavletich, N.P.

(2005) Mol Cell 20: 9-19

  • DOI: 10.1016/j.molcel.2005.09.003
  • Primary Citation of Related Structures:  
    2AST, 2ASS

  • PubMed Abstract: 

    • The ubiquitin-mediated proteolysis of the Cdk2 inhibitor p27(Kip1) plays a central role in cell cycle progression, and enhanced degradation of p27(Kip1) is associated with many common cancers. Proteolysis of p27(Kip1) is triggered by Thr187 phosphory ...

    The ubiquitin-mediated proteolysis of the Cdk2 inhibitor p27(Kip1) plays a central role in cell cycle progression, and enhanced degradation of p27(Kip1) is associated with many common cancers. Proteolysis of p27(Kip1) is triggered by Thr187 phosphorylation, which leads to the binding of the SCF(Skp2) (Skp1-Cul1-Rbx1-Skp2) ubiquitin ligase complex. Unlike other known SCF substrates, p27(Kip1) ubiquitination also requires the accessory protein Cks1. The crystal structure of the Skp1-Skp2-Cks1 complex bound to a p27(Kip1) phosphopeptide shows that Cks1 binds to the leucine-rich repeat (LRR) domain and C-terminal tail of Skp2, whereas p27(Kip1) binds to both Cks1 and Skp2. The phosphorylated Thr187 side chain of p27(Kip1) is recognized by a Cks1 phosphate binding site, whereas the side chain of an invariant Glu185 inserts into the interface between Skp2 and Cks1, interacting with both. The structure and biochemical data support the proposed model that Cdk2-cyclin A contributes to the recruitment of p27(Kip1) to the SCF(Skp2)-Cks1 complex.

    Organizational Affiliation: 

    Howard Hughes Medical Institute, New York, New York 10021, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
S-phase kinase-associated protein 1AA159Homo sapiensMutation(s): 1 
Gene Names: SKP1A, EMC19, OCP2, SKP1, TCEB1L
Find proteins for P63208 (Homo sapiens)
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Go to UniProtKB:  P63208
NIH Common Fund Data Resources
PHAROS  P63208
GTEx  ENSG00000113558
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
S-phase kinase-associated protein 2B336Homo sapiensMutation(s): 0 
Gene Names: SKP2, FBXL1
Find proteins for Q13309 (Homo sapiens)
Explore Q13309 
Go to UniProtKB:  Q13309
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PHAROS  Q13309
GTEx  ENSG00000145604
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinases regulatory subunit 1C69Homo sapiensMutation(s): 0 
Gene Names: CKS1, CKS1B, PNAS-143, PNAS-16
Find proteins for P61024 (Homo sapiens)
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Go to UniProtKB:  P61024
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PHAROS  P61024
GTEx  ENSG00000173207
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase inhibitor 1BD10N/AMutation(s): 0 
Find proteins for P46527 (Homo sapiens)
Explore P46527 
Go to UniProtKB:  P46527
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PHAROS  P46527
GTEx  ENSG00000111276
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEN
Query on BEN
Download Ideal Coordinates CCD File 
B, C
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO		DL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.7α = 90
b = 148.7β = 90
c = 98.8γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-18
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance