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- PDB-3brf: CSL (Lag-1) bound to DNA with Lin-12 RAM peptide, C2221 -

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Basic information

Entry
Database: PDB / ID: 3brf
TitleCSL (Lag-1) bound to DNA with Lin-12 RAM peptide, C2221
Components
  • DNA (5'-D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DCP*DCP*DCP*DAP*DCP*DAP*DGP*DT)-3')
  • DNA (5'-D(*DTP*DTP*DAP*DCP*DTP*DGP*DTP*DGP*DGP*DGP*DAP*DAP*DAP*DGP*DA)-3')
  • Lin-12 and glp-1 phenotype protein 1, isoform a
  • Protein lin-12
KeywordsDNA BINDING PROTEIN/DNA / protein-DNA complex / signaling / transcription / Notch / DNA-binding / ANK repeat / Developmental protein / Differentiation / EGF-like domain / Glycoprotein / Membrane / Transmembrane / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


Pre-NOTCH Processing in Golgi / NOTCH4 Activation and Transmission of Signal to the Nucleus / Negative regulation of NOTCH4 signaling / regulation of mesodermal cell fate specification / dauer exit / CSL-Notch-Mastermind transcription factor complex / positive regulation of mesodermal cell fate specification / regulation of vulval development / vulval development / cell projection morphogenesis ...Pre-NOTCH Processing in Golgi / NOTCH4 Activation and Transmission of Signal to the Nucleus / Negative regulation of NOTCH4 signaling / regulation of mesodermal cell fate specification / dauer exit / CSL-Notch-Mastermind transcription factor complex / positive regulation of mesodermal cell fate specification / regulation of vulval development / vulval development / cell projection morphogenesis / nematode larval development / regulation of basement membrane organization / egg-laying behavior / regulation of cell fate specification / sleep / Notch binding / cell fate specification / Notch signaling pathway / RNA polymerase II transcription regulator complex / transmembrane signaling receptor activity / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / apical plasma membrane / calcium ion binding / positive regulation of DNA-templated transcription / nucleus / plasma membrane
Similarity search - Function
: / LAG1, DNA binding domain / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein / NOD / NODP / Notch-like domain superfamily / LNR (Lin-12/Notch) repeat profile. ...: / LAG1, DNA binding domain / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein / NOD / NODP / Notch-like domain superfamily / LNR (Lin-12/Notch) repeat profile. / LNR domain / Notch domain / Domain found in Notch and Lin-12 / EGF-like, conserved site / Human growth factor-like EGF / EGF-like domain, extracellular / EGF-like domain / : / Calcium-binding EGF domain / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
sorbitol / DNA / DNA (> 10) / Protein lin-12 / :
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.47 Å
AuthorsWilson, J.J. / Kovall, R.A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: RAM-induced Allostery Facilitates Assembly of a Notch Pathway Active Transcription Complex.
Authors: Friedmann, D.R. / Wilson, J.J. / Kovall, R.A.
History
DepositionDec 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*DTP*DTP*DAP*DCP*DTP*DGP*DTP*DGP*DGP*DGP*DAP*DAP*DAP*DGP*DA)-3')
C: DNA (5'-D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DCP*DCP*DCP*DAP*DCP*DAP*DGP*DT)-3')
A: Lin-12 and glp-1 phenotype protein 1, isoform a
D: Protein lin-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0406
Polymers64,6764
Non-polymers3642
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.944, 95.972, 223.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-671-

HOH

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Components

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DNA chain , 2 types, 2 molecules BC

#1: DNA chain DNA (5'-D(*DTP*DTP*DAP*DCP*DTP*DGP*DTP*DGP*DGP*DGP*DAP*DAP*DAP*DGP*DA)-3')


Mass: 4673.059 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DCP*DCP*DCP*DAP*DCP*DAP*DGP*DT)-3')


Mass: 4503.949 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein / Protein/peptide / Sugars / Non-polymers , 4 types, 61 molecules AD

#3: Protein Lin-12 and glp-1 phenotype protein 1, isoform a / DNA-binding protein LAG-1 / Lag-1 protein


Mass: 53848.719 Da / Num. of mol.: 1 / Fragment: core domain
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): Rosetta2(DE3) / References: UniProt: Q9TYY1
#4: Protein/peptide Protein lin-12 / Abnormal cell lineage protein 12


Mass: 1649.974 Da / Num. of mol.: 1 / Fragment: RAM peptide
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: lin-12 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P14585
#5: Sugar ChemComp-SOR / sorbitol / D-sorbitol / D-glucitol


Type: D-saccharide / Mass: 182.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growTemperature: 277 K / Method: under oil microbatch / pH: 6
Details: Bis-Tris, MgCl2, PEG 3350, Sorbitol, pH 6.0, under oil microbatch, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1Bis11
2Tris11
3MgCl211
4PEG 335011
5Sorbitol11
6Bis12
7Tris12
8MgCl212
9PEG 335012
10Sorbitol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0094 Å
DetectorDetector: CCD / Date: Oct 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0094 Å / Relative weight: 1
ReflectionResolution: 2.47→50 Å / Num. obs: 24758 / % possible obs: 99.2 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.07 / Χ2: 1.011 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.47-2.563.80.54923250.91595.4
2.56-2.665.80.46624380.96598.8
2.66-2.785.70.32924581.04299.9
2.78-2.936.30.24324561.079100
2.93-3.1160.14824801.08499.9
3.11-3.356.10.10324781.14499.6
3.35-3.696.20.0724891.098100
3.69-4.226.40.05424910.98499.9
4.22-5.326.40.04625340.94499.8
5.32-5060.05226090.81698.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.3.0020refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→28.28 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.901 / SU B: 19.021 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.455 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1255 5.1 %RANDOM
Rwork0.23 ---
obs0.232 24719 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.915 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.47→28.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3489 609 24 57 4179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224272
X-RAY DIFFRACTIONr_angle_refined_deg1.4812.1355897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9135434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.81323.69168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.07615620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.251523
X-RAY DIFFRACTIONr_chiral_restr0.0930.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023005
X-RAY DIFFRACTIONr_nbd_refined0.2130.21595
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22809
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2182
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.27
X-RAY DIFFRACTIONr_mcbond_it0.4651.52211
X-RAY DIFFRACTIONr_mcangle_it0.83523516
X-RAY DIFFRACTIONr_scbond_it1.24632526
X-RAY DIFFRACTIONr_scangle_it1.8434.52379
LS refinement shellResolution: 2.47→2.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 71 -
Rwork0.388 1632 -
all-1703 -
obs--94.56 %

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