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- PDB-6wqu: CSL (RBPJ) bound to Notch3 RAM and DNA -

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Basic information

Entry
Database: PDB / ID: 6wqu
TitleCSL (RBPJ) bound to Notch3 RAM and DNA
Components
  • DNA (5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*GP*GP*T)-3')
  • DNA (5'-D(*TP*TP*AP*CP*CP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3')
  • Neurogenic locus notch homolog protein 3
  • Recombining binding protein suppressor of hairless
KeywordsTRANSCRIPTION/SIGNALING PROTEIN/DNA / Notch signaling / DNA binding protein / transcription factor / activation complex / TRANSCRIPTION / TRANSCRIPTION-SIGNALING PROTEIN-DNA complex
Function / homology
Function and homology information


glomerular capillary formation / 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 ...glomerular capillary formation / 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 / pulmonary valve development / positive regulation of cell proliferation involved in heart morphogenesis / Defective LFNG causes SCDO3 / dorsal aorta morphogenesis / sebaceous gland development / Pre-NOTCH Processing in the Endoplasmic Reticulum / endocardium morphogenesis / regulation of cell adhesion involved in heart morphogenesis / MAML1-RBP-Jkappa- ICN1 complex / aortic valve development / auditory receptor cell fate commitment / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / positive regulation of transcription of Notch receptor target / Notch-HLH transcription pathway / Noncanonical activation of NOTCH3 / epithelial to mesenchymal transition involved in endocardial cushion formation / heart induction / cardiac left ventricle morphogenesis / epidermal cell fate specification / pituitary gland development / neuroblast differentiation / endocardium development / atrioventricular canal development / Pre-NOTCH Processing in Golgi / neuron fate commitment / 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 / inflammatory response to antigenic stimulus / negative regulation of ossification / Notch binding / negative regulation of cold-induced thermogenesis / NOTCH3 Intracellular Domain Regulates Transcription / labyrinthine layer blood vessel development / artery morphogenesis / ventricular septum morphogenesis / Notch-HLH transcription pathway / heart looping / outflow tract morphogenesis / somatic stem cell population maintenance / negative regulation of cell differentiation / humoral immune response / hemopoiesis / negative regulation of neuron differentiation / epithelial to mesenchymal transition / blood vessel remodeling / cell fate commitment / somitogenesis / negative regulation of stem cell proliferation / keratinocyte differentiation / positive regulation of cardiac muscle cell proliferation / forebrain development / Notch signaling pathway / transcription repressor complex / B cell differentiation / epithelial cell proliferation / stem cell proliferation / positive regulation of epithelial cell proliferation / NOTCH3 Activation and Transmission of Signal to the Nucleus / protein-DNA complex / positive regulation of smooth muscle cell proliferation / axon guidance / neuron differentiation / Pre-NOTCH Transcription and Translation / positive regulation of miRNA transcription / positive regulation of canonical Wnt signaling pathway / signaling receptor activity / heart development / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / cell population proliferation / transcription regulator complex / sequence-specific DNA binding / cell differentiation / receptor complex / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to bacterium / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Golgi membrane / negative regulation of DNA-templated transcription / calcium ion binding
Similarity search - Function
Neurogenic locus Notch 3 / 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 ...Neurogenic locus Notch 3 / 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, C-terminal / Domain of unknown function / Notch / 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 / : / Calcium-binding EGF domain / Ankyrin repeats (many copies) / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / p53-like transcription factor, DNA-binding / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Ankyrin repeat / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
DNA / DNA (> 10) / Recombining binding protein suppressor of hairless / Neurogenic locus notch homolog protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsKovall, R.A. / Gagliani, E. / Hall, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA178974 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: PIM-induced phosphorylation of Notch3 promotes breast cancer tumorigenicity in a CSL-independent fashion.
Authors: Landor, S.K.J. / Santio, N.M. / Eccleshall, W.B. / Paramonov, V.M. / Gagliani, E.K. / Hall, D. / Jin, S.B. / Dahlstrom, K.M. / Salminen, T.A. / Rivero-Muller, A. / Lendahl, U. / Kovall, R.A. ...Authors: Landor, S.K.J. / Santio, N.M. / Eccleshall, W.B. / Paramonov, V.M. / Gagliani, E.K. / Hall, D. / Jin, S.B. / Dahlstrom, K.M. / Salminen, T.A. / Rivero-Muller, A. / Lendahl, U. / Kovall, R.A. / Koskinen, P.J. / Sahlgren, C.
History
DepositionApr 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
A: DNA (5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*GP*GP*T)-3')
B: DNA (5'-D(*TP*TP*AP*CP*CP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3')
C: Recombining binding protein suppressor of hairless
D: Neurogenic locus notch homolog protein 3


Theoretical massNumber of molelcules
Total (without water)59,3574
Polymers59,3574
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-29 kcal/mol
Surface area25290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.450, 97.660, 104.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*GP*GP*T)-3')


Mass: 4519.948 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*TP*TP*AP*CP*CP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3')


Mass: 4658.047 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein Recombining binding protein suppressor of hairless / J kappa-recombination signal-binding protein / RBP-J kappa / RBPJ


Mass: 47956.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rbpj, Igkjrb1, Igkrsbp, Rbpsuh / Production host: Escherichia coli (E. coli) / References: UniProt: P31266
#4: Protein/peptide Neurogenic locus notch homolog protein 3 / Notch 3


Mass: 2222.528 Da / Num. of mol.: 1 / Fragment: intracellular RAM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOTCH3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UM47
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 277.15 K / Method: microbatch / pH: 8 / Details: 0.2 M ammonium fluoride, 14% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.41→97.66 Å / Num. obs: 26714 / % possible obs: 99.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 54.53 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.05 / Rrim(I) all: 0.121 / Net I/σ(I): 9.7 / Num. measured all: 147091 / Scaling rejects: 21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.41-2.54.40.5831205027120.7050.2990.6592.797.7
9.02-97.665.10.06730405910.9930.0330.07517.598.2

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Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IAG

3iag


Resolution: 2.41→71.39 Å / Cor.coef. Fo:Fc: 0.9296 / Cor.coef. Fo:Fc free: 0.9153 / SU R Cruickshank DPI: 0.305 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.316 / SU Rfree Blow DPI: 0.222 / SU Rfree Cruickshank DPI: 0.221
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 1349 5.06 %RANDOM
Rwork0.1988 ---
obs0.2005 26661 98.85 %-
Displacement parametersBiso max: 118.69 Å2 / Biso mean: 38.78 Å2 / Biso min: 16.53 Å2
Baniso -1Baniso -2Baniso -3
1--4.1589 Å20 Å20 Å2
2--2.7929 Å20 Å2
3---1.3659 Å2
Refine analyzeLuzzati coordinate error obs: 0.314 Å
Refinement stepCycle: final / Resolution: 2.41→71.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3417 609 0 105 4131
Biso mean---32.46 -
Num. residues----462
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1370SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes80HARMONIC2
X-RAY DIFFRACTIONt_gen_planes533HARMONIC5
X-RAY DIFFRACTIONt_it4175HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion540SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4329SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4175HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5770HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.15
X-RAY DIFFRACTIONt_other_torsion20.11
LS refinement shellResolution: 2.41→2.51 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.3042 135 4.73 %
Rwork0.2431 2720 -
all0.246 2855 -
obs--95.05 %

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