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- PDB-1ttu: Crystal Structure of CSL bound to DNA -

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Basic information

Entry
Database: PDB / ID: 1ttu
TitleCrystal Structure of CSL bound to DNA
Components
  • 5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)-3'
  • 5'-D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3'
  • lin-12 And Glp-1 transcriptional regulator
KeywordsTRANSCRIPTION / beta-trefoil domain / protein-DNA complex / rel homology region / CSL / Notch signaling / transcription factor
Function / homology
Function and homology information


stem cell fate determination / regulation of mesodermal cell fate specification / dauer exit / positive regulation of vulval development / CSL-Notch-Mastermind transcription factor complex / cell projection morphogenesis / oocyte growth / nematode larval development / germ-line stem cell division / egg-laying behavior ...stem cell fate determination / regulation of mesodermal cell fate specification / dauer exit / positive regulation of vulval development / CSL-Notch-Mastermind transcription factor complex / cell projection morphogenesis / oocyte growth / nematode larval development / germ-line stem cell division / egg-laying behavior / regulation of cell fate specification / cell fate determination / Notch binding / cell fate specification / Notch signaling pathway / transcription coactivator binding / positive regulation of miRNA transcription / RNA polymerase II transcription regulator complex / regulation of gene expression / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
LAG1, DNA binding domain / Beta-trefoil DNA-binding domain / RBP-J/Cbf11/Cbf12, DNA binding / Beta-trefoil domain superfamily / RBP-J/Cbf11, DNA binding domain superfamily / RBP-Jkappa, IPT domain / Suppressor of hairless-like / Beta-trefoil DNA-binding domain / LAG1, DNA binding / TIG domain ...LAG1, DNA binding domain / Beta-trefoil DNA-binding domain / RBP-J/Cbf11/Cbf12, DNA binding / Beta-trefoil domain superfamily / RBP-J/Cbf11, DNA binding domain superfamily / RBP-Jkappa, IPT domain / Suppressor of hairless-like / Beta-trefoil DNA-binding domain / LAG1, DNA binding / TIG domain / LAG1, DNA binding / Beta-trefoil DNA-binding domain / p53-like transcription factor, DNA-binding / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / : / Suppressor of hairless protein homolog
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.85 Å
AuthorsKovall, R.A. / Hendrickson, W.A.
CitationJournal: Embo J. / Year: 2004
Title: Crystal structure of the nuclear effector of Notch signaling, CSL, bound to DNA
Authors: Kovall, R.A. / Hendrickson, W.A.
History
DepositionJun 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
B: 5'-D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3'
C: 5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)-3'
A: lin-12 And Glp-1 transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,49712
Polymers62,9393
Non-polymers5599
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.547, 127.547, 97.604
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: DNA chain 5'-D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3'


Mass: 4673.059 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The sequence comes from a region within the mammalian HES-1 promoter
#2: DNA chain 5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)-3'


Mass: 4503.949 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The sequence comes from a region within the mammalian HES-1 promoter
#3: Protein lin-12 And Glp-1 transcriptional regulator / CLS


Mass: 53761.641 Da / Num. of mol.: 1 / Fragment: conserved core (residues 192-663)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: lag-1 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q9TYY1, UniProt: V6CLJ5*PLUS
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 3.648 Å3/Da / Density % sol: 64.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: MES, ammonium sulfate, PEG 20K, ethylene glycol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2ammonium sulfate11
3PEG 20K11
4ethylene glycol11

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 31-ID10.9791, 0.9793, 0.9795, 0.9686
SYNCHROTRONNSLS X4A20.9792
Detector
TypeIDDetector
MARRESEARCH1CCD
ADSC QUANTUM 42CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97931
30.97951
40.96861
50.97921
ReflectionResolution: 2.8→20 Å / Num. all: 22264 / Num. obs: 22264 / % possible obs: 99.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 89.1 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 23.2
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.313 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.85→19.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1124715.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2085 9.9 %RANDOM
Rwork0.201 ---
obs0.201 21051 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.2202 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 68.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.82 Å215.55 Å20 Å2
2--2.82 Å20 Å2
3----5.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.85→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 609 36 46 4163
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_mcbond_it5.761.5
X-RAY DIFFRACTIONc_mcangle_it8.482
X-RAY DIFFRACTIONc_scbond_it8.832
X-RAY DIFFRACTIONc_scangle_it11.492.5
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.408 364 10.3 %
Rwork0.316 3162 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3GLYCOL.PARAM
X-RAY DIFFRACTION4WATER_REP.PARAM

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