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- PDB-3c2h: Crystal Structure of SYS-1 at 2.6A resolution -

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Basic information

Entry
Database: PDB / ID: 3c2h
TitleCrystal Structure of SYS-1 at 2.6A resolution
ComponentsSys-1 protein
KeywordsCELL ADHESION / SYS-1 / Caenorhabditis elegans / beta-catenin / WNT
Function / homology
Function and homology information


polarity specification of proximal/distal axis / gonad morphogenesis / positive regulation of mesodermal cell fate specification / mesodermal cell fate specification / regulation of asymmetric cell division / gonad development / endodermal cell fate commitment / proximal/distal pattern formation / embryonic digestive tract development / embryo development ending in birth or egg hatching ...polarity specification of proximal/distal axis / gonad morphogenesis / positive regulation of mesodermal cell fate specification / mesodermal cell fate specification / regulation of asymmetric cell division / gonad development / endodermal cell fate commitment / proximal/distal pattern formation / embryonic digestive tract development / embryo development ending in birth or egg hatching / female gonad development / kinetochore / Wnt signaling pathway / male gonad development / cell cortex / scaffold protein binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / negative regulation of gene expression / centrosome / negative regulation of DNA-templated transcription / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Sys-1 C-terminal domain-like / 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
CITRATE ANION / SYmmetrical Sister cell hermaphrodite gonad defect
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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: Genetics / Year: 2004
Title: The sys-1 and sys-3 genes cooperate with Wnt signaling to establish the proximal-distal axis of the Caenorhabditis elegans gonad.
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 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,4247
Polymers141,8672
Non-polymers5575
Water70339
1
A: Sys-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3074
Polymers70,9331
Non-polymers3733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sys-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1183
Polymers70,9331
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)203.500, 95.048, 149.390
Angle α, β, γ (deg.)90.000, 124.710, 90.000
Int Tables number5
Space group name H-MC121
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
11METMETALAALAAA180 - 2191 - 40
21METMETALAALABB180 - 2191 - 40
32ASNASNMETMETAA225 - 59046 - 411
42ASNASNMETMETBB225 - 59046 - 411
53LYSLYSCYSCYSAA600 - 628421 - 449
63LYSLYSCYSCYSBB600 - 628421 - 449
74METMETLEULEUAA631 - 734452 - 555
84METMETLEULEUBB631 - 734452 - 555
95PROPROLEULEUAA742 - 792563 - 613
105PROPROLEULEUBB742 - 792563 - 613

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Components

#1: Protein Sys-1 protein


Mass: 70933.336 Da / Num. of mol.: 2 / Fragment: Armadillor 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: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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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: 4.19 Å3/Da / Density % sol: 70.61 %
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 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 70425 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.065 / Χ2: 1.155 / Net I/σ(I): 10.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.437 / Num. unique all: 6527 / Χ2: 1.033 / % possible all: 91.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.56 Å
Translation2.5 Å49.56 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVEphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→49.57 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.065 / SU ML: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.391 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.286 3573 5.1 %RANDOM
Rwork0.245 ---
all0.2466 72547 --
obs0.247 70332 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.547 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å20 Å20.12 Å2
2--0.34 Å20 Å2
3---1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9770 0 37 39 9846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210026
X-RAY DIFFRACTIONr_angle_refined_deg1.141.96713646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.00351231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.89224.279437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.85151716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8271559
X-RAY DIFFRACTIONr_chiral_restr0.0880.21584
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027501
X-RAY DIFFRACTIONr_nbd_refined0.2060.24735
X-RAY DIFFRACTIONr_nbtor_refined0.3060.27024
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.210
X-RAY DIFFRACTIONr_mcbond_it0.90726386
X-RAY DIFFRACTIONr_mcangle_it1.655310115
X-RAY DIFFRACTIONr_scbond_it1.84344082
X-RAY DIFFRACTIONr_scangle_it2.96463531
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3282 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.265
LOOSE THERMAL1.4210
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 239 -
Rwork0.333 4516 -
all-4755 -
obs--90.26 %

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