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- PDB-3c2g: Crystal complex of SYS-1/POP-1 at 2.5A resolution -

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Basic information

Entry
Database: PDB / ID: 3c2g
TitleCrystal complex of SYS-1/POP-1 at 2.5A resolution
Components
  • Pop-1 8-residue peptide
  • Sys-1 protein
KeywordsCELL ADHESION/TRANSCRIPTION / beta-catenin / phylogeny / SYS-1 / POP-1 / Caenorhabditis elegans / Developmental protein / DNA-binding / Nucleus / CELL ADHESION-TRANSCRIPTION COMPLEX
Function / homology
Function and homology information


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 / Formation of the beta-catenin:TCF transactivating complex / Transcriptional Regulation by VENTX / RUNX3 regulates WNT signaling / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation ...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 / Formation of the beta-catenin:TCF transactivating complex / Transcriptional Regulation by VENTX / RUNX3 regulates WNT signaling / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Deactivation of the beta-catenin transactivating complex / gonad morphogenesis / nematode pharyngeal muscle development / Ca2+ pathway / positive regulation of mesodermal cell fate specification / mesodermal cell fate specification / regulation of asymmetric cell division / asymmetric cell division / mitochondrial unfolded protein response / gonad development / beta-catenin-TCF complex / 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 / cell fate determination / embryo development ending in birth or egg hatching / cell fate specification / female gonad development / histone acetyltransferase binding / canonical Wnt signaling pathway / negative regulation of stem cell proliferation / transcription corepressor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / beta-catenin binding / kinetochore / histone deacetylase binding / male gonad development / Wnt signaling pathway / transcription corepressor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / scaffold protein binding / cell cortex / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / 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 / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Sys-1 C-terminal domain-like / c-clamp / Transcription factor TCF/LEF / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant ...Sys-1 C-terminal domain-like / c-clamp / Transcription factor TCF/LEF / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Arc Repressor Mutant, subunit A / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein pop-1 / Beta-catenin homolog sys-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsLiu, J. / Phillips, B.T. / Amaya, M.F. / Kimble, J. / Xu, W.
Citation
Journal: Dev.Cell / Year: 2008
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: Journal: Cell(Cambridge,Mass.) / Year: 2005
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: Journal: DEV.BIOL. / Year: 2001
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: Journal: Proc.Natl.Acad.Sci.USA / Year: 2007
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: Journal: Development / Year: 2007
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
DepositionJan 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sys-1 protein
B: Sys-1 protein
C: Pop-1 8-residue peptide
D: Pop-1 8-residue peptide


Theoretical massNumber of molelcules
Total (without water)145,1764
Polymers145,1764
Non-polymers00
Water1,29772
1
A: Sys-1 protein
C: Pop-1 8-residue peptide


Theoretical massNumber of molelcules
Total (without water)72,5882
Polymers72,5882
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
MethodPISA
2
B: Sys-1 protein
D: Pop-1 8-residue peptide


Theoretical massNumber of molelcules
Total (without water)72,5882
Polymers72,5882
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.969, 85.343, 93.657
Angle α, β, γ (deg.)65.220, 78.080, 83.020
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11MSEMSEALAALAAA180 - 2191 - 40
21MSEMSEALAALABB180 - 2191 - 40
32ASNASNMSEMSEAA225 - 59046 - 411
42ASNASNMSEMSEBB225 - 59046 - 411
53LYSLYSCYSCYSAA600 - 628421 - 449
63LYSLYSCYSCYSBB600 - 628421 - 449
74MSEMSELEULEUAA631 - 734452 - 555
84MSEMSELEULEUBB631 - 734452 - 555
95PROPROLEULEUAA742 - 792563 - 613
105PROPROLEULEUBB742 - 792563 - 613

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Components

#1: Protein Sys-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.) Caenorhabditis elegans (invertebrata) / Gene: SYS-1 / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9XVI2
#2: Protein/peptide Pop-1 8-residue 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.) Caenorhabditis elegans (invertebrata) / Gene: POP-1 / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q10666
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.15 Å3/Da / Density % sol: 70.38 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 31, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.5→2.59 Å / % possible all: 72.8

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Phasing

PhasingMethod: SAD
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 81642
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
12.6-10032.90.912594
8.91-12.6200.9541132
7.27-8.9121.90.9441452
6.3-7.2728.70.9161682
5.64-6.329.20.9181902
5.14-5.6428.10.9262103
4.76-5.1423.60.9342270
4.45-4.76230.9362422
4.2-4.4523.50.9342576
3.98-4.224.80.9232756
3.8-3.9826.50.9122938
3.64-3.827.30.912981
3.49-3.6431.90.8993210
3.37-3.4935.10.8893342
3.25-3.3737.40.8863508
3.15-3.25390.8743567
3.06-3.1543.10.8783757
2.97-3.0648.30.8723860
2.89-2.97520.8723943
2.82-2.89550.8563938
2.75-2.8283.80.8313828
2.69-2.7592.80.8233812
2.63-2.6990.70.8083627
2.57-2.6388.80.7923382
2.52-2.5788.20.7763137
2.47-2.5289.10.7622923
2.42-2.4790.20.7242528
2.38-2.4290.70.7042183
2.32-2.3891.70.6582289

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
DM6phasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 2.5→48 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.903 / SU B: 7.633 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.314 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 3763 5 %RANDOM
Rwork0.216 ---
obs0.218 75483 93.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.676 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å21.65 Å20.24 Å2
2--0.89 Å2-0.6 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9885 0 0 72 9957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02210110
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.96413757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.90351242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.77924.086443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.012151739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8971564
X-RAY DIFFRACTIONr_chiral_restr0.0890.21601
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027564
X-RAY DIFFRACTIONr_nbd_refined0.2060.24612
X-RAY DIFFRACTIONr_nbtor_refined0.3060.27124
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.23
X-RAY DIFFRACTIONr_mcbond_it1.15926471
X-RAY DIFFRACTIONr_mcangle_it1.886310209
X-RAY DIFFRACTIONr_scbond_it2.4344094
X-RAY DIFFRACTIONr_scangle_it3.74463548
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3262 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.325
LOOSE THERMAL2.1910
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 198 -
Rwork0.281 3894 -
all-4092 -
obs--68.89 %

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