3C2G

Crystal complex of SYS-1/POP-1 at 2.5A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The C. elegans SYS-1 protein is a bona fide beta-catenin.

Liu, J.Phillips, B.T.Amaya, M.F.Kimble, J.Xu, W.

(2008) Dev Cell 14: 751-761

  • DOI: 10.1016/j.devcel.2008.02.015
  • Primary Citation of Related Structures:  
    3C2G, 3C2H

  • PubMed Abstract: 
  • C. elegans SYS-1 has key functional characteristics of a canonical beta-catenin, but no significant sequence similarity. Here, we report the SYS-1 crystal structure, both on its own and in a complex with POP-1, the C. elegans TCF homolog. The two str ...

    C. elegans SYS-1 has key functional characteristics of a canonical beta-catenin, but no significant sequence similarity. Here, we report the SYS-1 crystal structure, both on its own and in a complex with POP-1, the C. elegans TCF homolog. The two structures possess signature features of canonical beta-catenin and the beta-catenin/TCF complex that could not be predicted by sequence. Most importantly, SYS-1 bears 12 armadillo repeats and the SYS-1/POP-1 interface is anchored by a conserved salt-bridge, the "charged button." We also modeled structures for three other C. elegans beta-catenins to predict the molecular basis of their distinct binding properties. Finally, we generated a phylogenetic tree, using the region of highest structural similarity between SYS-1 and beta-catenin, and found that SYS-1 clusters robustly within the beta-catenin clade. We conclude that the SYS-1 protein belongs to the beta-catenin family and suggest that additional divergent beta-catenins await discovery.


    Related Citations: 
    • A beta-catenin identified by functional rather than sequence criteria and its role in Wnt/MAPK signaling.
      Miskowski, J., Li, Y., Kimble, J.
      (2005) Cell 121: 761
    • The sys-1 gene and sexual dimorphism during gonadogenesis in Caenorhabditis elegans.
      Kidd III, A.R., Miskowski, J.A., Siegfried, K.R., Sawa, H., Kimble, J.
      (2001) Dev Biol 230: 61
    • Reciprocal asymmetry of SYS-1/beta-catenin and POP-1/TCF controls asymmetric divisions in Caenorhabditis elegans.
      Phillips, B.T., Kidd III, A.R., King, R., Hardin, J., Kimble, J.
      (2007) Proc Natl Acad Sci U S A 104: 3231
    • Binary cell fate specification during C. elegans embryogenesis driven by reiterated reciprocal asymmetry of TCF POP-1 and its coactivator beta-catenin SYS-1.
      Huang, S., Shetty, P., Robertson, S.M., Lin, R.
      (2007) Development 134: 2685

    Organizational Affiliation

    Department of Biological Structure, University of Washington, Seattle, WA 98195-7420, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sys-1 proteinAB619N/AMutation(s): 0 
Gene Names: SYS-1
Find proteins for Q9XVI2 (Caenorhabditis elegans)
Explore Q9XVI2 
Go to UniProtKB:  Q9XVI2
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pop-1 8-residue peptideCD8N/AMutation(s): 0 
Gene Names: POP-1
Find proteins for Q10666 (Caenorhabditis elegans)
Explore Q10666 
Go to UniProtKB:  Q10666
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.969α = 65.22
b = 85.343β = 78.08
c = 93.657γ = 83.02
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description