1P22

Structure of a beta-TrCP1-Skp1-beta-catenin complex: destruction motif binding and lysine specificity on the SCFbeta-TrCP1 ubiquitin ligase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 

wwPDB Validation 3D Report Full Report


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


Literature

Structure of a beta-TrCP1-Skp1-beta-Catenin complex: destruction motif binding and lysine specificity of the SCFbeta-TrCP1 ubiquitin ligase

Wu, G., Xu, G., Schulman, B.A., Jeffrey, P.D., Harper, J.W., Pavletich, N.P.

(2003) Mol Cell 11: 1445-1456

  • DOI: 10.1016/s1097-2765(03)00234-x
  • Primary Citation of Related Structures:  
    1P22

  • PubMed Abstract: 

    • The SCF ubiquitin ligases catalyze protein ubiquitination in diverse cellular processes. SCFs bind substrates through the interchangeable F box protein subunit, with the >70 human F box proteins allowing the recognition of a wide range of substrates. ...

    The SCF ubiquitin ligases catalyze protein ubiquitination in diverse cellular processes. SCFs bind substrates through the interchangeable F box protein subunit, with the >70 human F box proteins allowing the recognition of a wide range of substrates. The F box protein beta-TrCP1 recognizes the doubly phosphorylated DpSGphiXpS destruction motif, present in beta-catenin and IkappaB, and directs the SCF(beta-TrCP1) to ubiquitinate these proteins at specific lysines. The 3.0 A structure of a beta-TrCP1-Skp1-beta-catenin complex reveals the basis of substrate recognition by the beta-TrCP1 WD40 domain. The structure, together with the previous SCF(Skp2) structure, leads to the model of SCF catalyzing ubiquitination by increasing the effective concentration of the substrate lysine at the E2 active site. The model's prediction that the lysine-destruction motif spacing is a determinant of ubiquitination efficiency is confirmed by measuring ubiquitination rates of mutant beta-catenin peptides, solidifying the model and also providing a mechanistic basis for lysine selection.

    Organizational Affiliation: 

    Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
F-box/WD-repeat protein 1AA435Homo sapiensMutation(s): 0 
Gene Names: BTRC, BTRCP, FBW1A, FBXW1A
Find proteins for Q9Y297 (Homo sapiens)
Explore Q9Y297 
Go to UniProtKB:  Q9Y297
NIH Common Fund Data Resources
PHAROS  Q9Y297
GTEx  ENSG00000166167
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Skp1B145Homo sapiensMutation(s): 0 
Gene Names: SKP1, EMC19, OCP2, SKP1A, TCEB1L
Find proteins for P63208 (Homo sapiens)
Explore P63208 
Go to UniProtKB:  P63208
NIH Common Fund Data Resources
PHAROS  P63208
GTEx  ENSG00000113558
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-cateninC26Homo sapiensMutation(s): 2 
Gene Names: CTNNB1 OR CTNNB, CTNNB1, CTNNB, OK/SW-cl.35, PRO2286
Find proteins for P35222 (Homo sapiens)
Explore P35222 
Go to UniProtKB:  P35222
NIH Common Fund Data Resources
PHAROS  P35222
GTEx  ENSG00000168036
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP		CL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.6α = 90
b = 82.6β = 90
c = 111.5γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
DMmodel building
REFMACrefinement
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-08
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance