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- PDB-3brg: CSL (RBP-Jk) bound to DNA -

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Basic information

Entry
Database: PDB / ID: 3brg
TitleCSL (RBP-Jk) bound to DNA
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')
  • Recombining binding protein suppressor of hairless
KeywordsDNA BINDING PROTEIN/DNA / protein-DNA complex / signaling / transcription / Notch / Activator / Alternative splicing / DNA-binding / Notch signaling pathway / Nucleus / Repressor / Transcription regulation / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


determination of heart left/right asymmetry / regulation of generation of precursor metabolites and energy / blood vessel endothelial cell fate specification / positive regulation of ERBB signaling pathway / club cell differentiation / arterial endothelial cell fate commitment / blood vessel lumenization / regulation of timing of cell differentiation / regulation of reproductive process / positive regulation of ephrin receptor signaling pathway ...determination of heart left/right asymmetry / regulation of generation of precursor metabolites and energy / blood vessel endothelial cell fate specification / positive regulation of ERBB signaling pathway / club cell differentiation / arterial endothelial cell fate commitment / blood vessel lumenization / regulation of timing of cell differentiation / regulation of reproductive process / positive regulation of ephrin receptor signaling pathway / secondary heart field specification / positive regulation of cell proliferation involved in heart morphogenesis / pulmonary valve development / dorsal aorta morphogenesis / sebaceous gland development / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / endocardium morphogenesis / regulation of cell adhesion involved in heart morphogenesis / Notch-HLH transcription pathway / MAML1-RBP-Jkappa- ICN1 complex / aortic valve development / auditory receptor cell fate commitment / positive regulation of transcription of Notch receptor target / epithelial to mesenchymal transition involved in endocardial cushion formation / heart induction / cardiac left ventricle morphogenesis / epidermal cell fate specification / pituitary gland development / endocardium development / atrioventricular canal development / cardiac muscle cell myoblast differentiation / hair follicle maturation / myeloid dendritic cell differentiation / ventricular trabecula myocardium morphogenesis / positive regulation of BMP signaling pathway / regulation of epithelial cell proliferation / negative regulation of ossification / inflammatory response to antigenic stimulus / artery morphogenesis / negative regulation of cold-induced thermogenesis / labyrinthine layer blood vessel development / ventricular septum morphogenesis / heart looping / outflow tract morphogenesis / somatic stem cell population maintenance / negative regulation of cell differentiation / humoral immune response / hemopoiesis / epithelial to mesenchymal transition / blood vessel remodeling / cell fate commitment / somitogenesis / negative regulation of stem cell proliferation / keratinocyte differentiation / Notch signaling pathway / positive regulation of cardiac muscle cell proliferation / transcription repressor complex / B cell differentiation / epithelial cell proliferation / stem cell proliferation / positive regulation of epithelial cell proliferation / protein-DNA complex / neuron differentiation / positive regulation of canonical Wnt signaling pathway / heart development / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / DNA-binding transcription factor binding / cell population proliferation / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to bacterium / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / protein-containing complex binding / positive regulation of gene expression / nucleolus / 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 / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm
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) / Recombining binding protein suppressor of hairless
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsFriedmann, D.R. / 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
A: DNA (5'-D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DCP*DCP*DCP*DAP*DCP*DAP*DGP*DT)-3')
B: DNA (5'-D(*DTP*DTP*DAP*DCP*DTP*DGP*DTP*DGP*DGP*DGP*DAP*DAP*DAP*DGP*DA)-3')
C: Recombining binding protein suppressor of hairless
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,20315
Polymers57,4583
Non-polymers74512
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.769, 95.388, 113.695
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: 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
#2: 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
#3: Protein Recombining binding protein suppressor of hairless / J kappa-recombination signal-binding protein / RBP-J kappa


Mass: 48281.082 Da / Num. of mol.: 1 / Fragment: core domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rbpj, Igkjrb1, Igkrsbp, Rbpsuh / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P31266
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 3.15 Å3/Da / Density % sol: 60.96 %
Crystal growTemperature: 277 K / Method: under oil microbatch / pH: 5.5
Details: Bis-Tris, Sodium Chloride, PEG 3350, Xylitol, pH 5.5, under oil microbatch, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1Bis11
2Tris11
3Sodium Chloride11
4PEG 335011
5Xylitol11
6Bis12
7Tris12
8Sodium Chloride12
9PEG 335012
10Xylitol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorDetector: CCD / Date: Mar 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 37593 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 19.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.2-2.286.30.271100
2.28-2.376.70.293100
2.37-2.486.80.197100
2.48-2.616.90.144100
2.61-2.776.90.098100
2.77-2.996.80.072100
2.99-3.296.90.059100
3.29-3.766.60.0599.9
3.76-4.746.80.037100
4.74-506.40.03499.1

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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: 2.2→32.06 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 11.741 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25515 1876 5 %RANDOM
Rwork0.21894 ---
obs0.22079 35675 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.695 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3290 609 48 134 4081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224078
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6352.1615611
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8045411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03724.079152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.00715604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2811522
X-RAY DIFFRACTIONr_chiral_restr0.1140.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022835
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.21565
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22603
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2200
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0410.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.811.52119
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36623335
X-RAY DIFFRACTIONr_scbond_it1.73432435
X-RAY DIFFRACTIONr_scangle_it2.6384.52276
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 139 -
Rwork0.314 2557 -
obs--99.93 %

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