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- PDB-3brd: CSL (Lag-1) bound to DNA with Lin-12 RAM peptide, P212121 -

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Basic information

Entry
Database: PDB / ID: 3brd
TitleCSL (Lag-1) bound to DNA with Lin-12 RAM peptide, P212121
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


stem cell fate determination / 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 / positive regulation of vulval development / CSL-Notch-Mastermind transcription factor complex / cell projection morphogenesis / positive regulation of mesodermal cell fate specification ...stem cell fate determination / 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 / positive regulation of vulval development / CSL-Notch-Mastermind transcription factor complex / cell projection morphogenesis / positive regulation of mesodermal cell fate specification / vulval development / regulation of vulval development / oocyte growth / nematode larval development / germ-line stem cell division / regulation of basement membrane organization / egg-laying behavior / regulation of cell fate specification / cell fate determination / sleep / Notch binding / cell fate specification / Notch signaling pathway / transcription coactivator binding / positive regulation of miRNA transcription / RNA polymerase II transcription regulator complex / transmembrane signaling receptor activity / double-stranded DNA binding / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / apical plasma membrane / RNA polymerase II cis-regulatory region sequence-specific DNA binding / calcium ion 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 / plasma membrane
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 / 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-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / p53-like transcription factor, DNA-binding / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / 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 / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein lin-12 / : / Suppressor of hairless protein homolog
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.21 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 1.3Feb 21, 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: 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)67,08114
Polymers66,4614
Non-polymers62110
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.153, 98.866, 126.313
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 , 2 types, 2 molecules AD

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


Mass: 53761.641 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, UniProt: V6CLJ5*PLUS
#4: Protein/peptide Protein lin-12 / Abnormal cell lineage protein 12


Mass: 3522.095 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

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Non-polymers , 2 types, 141 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 277 K / Method: under oil microbatch / pH: 5.5
Details: Bis-Tris, Ammonium Sulfate, PEG 3350, Ethylene Glycol, pH 5.5, under oil microbatch, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1Bis11
2Tris11
3Ammonium Sulfate11
4PEG 335011
5Ethylene Glycol11
6Bis12
7Tris12
8Ammonium Sulfate12
9PEG 335012
10Ethylene Glycol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97934 Å
DetectorDetector: CCD / Date: Oct 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 36557 / % possible obs: 94.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.066 / Χ2: 1.062 / Net I/σ(I): 14.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.2850.34526891.07371.3
2.28-2.374.80.30631941.13984.1
2.37-2.485.10.26935621.15393.6
2.48-2.615.60.23737811.12899.5
2.61-2.775.90.17538121.124100
2.77-2.995.80.12338511.036100
2.99-3.295.80.0838230.94699.8
3.29-3.765.80.07538721.031100
3.76-4.745.70.05639011.018100
4.74-505.40.04240721.02299

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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: 2.21→39.87 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 12.004 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1819 5 %RANDOM
Rwork0.208 ---
obs0.211 36498 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.242 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.21→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3548 609 40 131 4328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224339
X-RAY DIFFRACTIONr_angle_refined_deg1.7952.135969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6995440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20923.642173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.615633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2931525
X-RAY DIFFRACTIONr_chiral_restr0.1220.2655
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023051
X-RAY DIFFRACTIONr_nbd_refined0.2080.21527
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22805
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2224
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.280.210
X-RAY DIFFRACTIONr_mcbond_it0.8661.52259
X-RAY DIFFRACTIONr_mcangle_it1.48723569
X-RAY DIFFRACTIONr_scbond_it1.93132570
X-RAY DIFFRACTIONr_scangle_it2.6954.52398
LS refinement shellResolution: 2.21→2.264 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 84 -
Rwork0.267 1820 -
all-1904 -
obs--67.37 %

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