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Open data
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Basic information
Entry | Database: PDB / ID: 3c2g | ||||||
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Title | Crystal complex of SYS-1/POP-1 at 2.5A resolution | ||||||
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![]() | CELL ADHESION/TRANSCRIPTION / beta-catenin / phylogeny / SYS-1 / POP-1 / Caenorhabditis elegans / Developmental protein / DNA-binding / Nucleus / CELL ADHESION-TRANSCRIPTION COMPLEX | ||||||
Function / homology | ![]() chordate pharyngeal muscle development / regulation of neuroblast migration / regulation of defecation rhythm / mesodermal cell fate determination / Repression of WNT target genes / polarity specification of proximal/distal axis / positive regulation of vulval development / Transcriptional Regulation by VENTX / RUNX3 regulates WNT signaling / Deactivation of the beta-catenin transactivating complex ...chordate pharyngeal muscle development / regulation of neuroblast migration / regulation of defecation rhythm / mesodermal cell fate determination / Repression of WNT target genes / polarity specification of proximal/distal axis / positive regulation of vulval development / Transcriptional Regulation by VENTX / RUNX3 regulates WNT signaling / Deactivation of the beta-catenin transactivating complex / gonad morphogenesis / Formation of the beta-catenin:TCF transactivating complex / Ca2+ pathway / positive regulation of mesodermal cell fate specification / mesodermal cell fate specification / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / regulation of asymmetric cell division / asymmetric cell division / gonad development / endodermal cell fate commitment / proximal/distal pattern formation / negative regulation of cell division / embryonic digestive tract development / regulation of cell fate specification / embryonic pattern specification / embryo development ending in birth or egg hatching / histone acetyltransferase binding / female gonad development / transcription factor binding / canonical Wnt signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / kinetochore / Wnt signaling pathway / histone deacetylase binding / beta-catenin binding / male gonad development / cell cortex / scaffold protein binding / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / centrosome / positive regulation of gene expression / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, J. / Phillips, B.T. / Amaya, M.F. / Kimble, J. / Xu, W. | ||||||
![]() | ![]() Title: The C. elegans SYS-1 protein is a bona fide beta-catenin. Authors: Liu, J. / Phillips, B.T. / Amaya, M.F. / Kimble, J. / Xu, W. #1: ![]() Title: A beta-catenin identified by functional rather than sequence criteria and its role in Wnt/MAPK signaling. Authors: Miskowski, J. / Li, Y. / Kimble, J. #2: ![]() Title: The sys-1 gene and sexual dimorphism during gonadogenesis in Caenorhabditis elegans. Authors: Kidd III, A.R. / Miskowski, J.A. / Siegfried, K.R. / Sawa, H. / Kimble, J. #3: ![]() Title: Reciprocal asymmetry of SYS-1/beta-catenin and POP-1/TCF controls asymmetric divisions in Caenorhabditis elegans. Authors: Phillips, B.T. / Kidd III, A.R. / King, R. / Hardin, J. / Kimble, J. #4: ![]() Title: Binary cell fate specification during C. elegans embryogenesis driven by reiterated reciprocal asymmetry of TCF POP-1 and its coactivator beta-catenin SYS-1. Authors: Huang, S. / Shetty, P. / Robertson, S.M. / Lin, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 248.8 KB | Display | ![]() |
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PDB format | ![]() | 207.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 6
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Components
#1: Protein | Mass: 71636.766 Da / Num. of mol.: 2 / Fragment: Armadillo Domain (UNP residues 180 - 798) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 951.078 Da / Num. of mol.: 2 / Fragment: Beta-catenin Binding Domain (UNP residues 8 - 15) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.15 Å3/Da / Density % sol: 70.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM Hepes, 0.6 M Na/K Tartrate, 20 mM Glycine and 5mM DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 31, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 75516 / Num. obs: 75516 / % possible obs: 93.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 72.8 |
-Phasing
Phasing | Method: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing dm | Method: Solvent flattening and Histogram matching / Reflection: 81642 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.676 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→48 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3262 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.502→2.567 Å / Total num. of bins used: 20
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