Biological Assembly 1  

 3D View: Structure

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: 69.20 kDa 
• Atom Count: 4340 
• Residue Count: 606 
• Unique protein chains: 3

1P22

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

• DOI: 10.2210/pdb1P22/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2003-04-14 Released: 2003-07-08 
• Deposition Author(s): Wu, G., Xu, G., Schulman, B.A., Jeffrey, P.D., Harper, J.W., Pavletich, N.P.

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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 

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

• PubMed: 12820959 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F-box/WD-repeat protein 1A	A	435	Homo sapiens	Mutation(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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Skp1	B	145	Homo sapiens	Mutation(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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-catenin	C	26	Homo sapiens	Mutation(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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	C	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

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 = 82.6	α = 90
b = 82.6	β = 90
c = 111.5	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
DM	model building
REFMAC	refinement
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-04-14 
• Released Date: 2003-07-08 
Deposition Author(s): Wu, G., Xu, G., Schulman, B.A., Jeffrey, P.D., Harper, J.W., Pavletich, N.P.

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