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- PDB-5eg6: CSL-RITA complex bound to DNA -

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Basic information

Entry
Database: PDB / ID: 5eg6
TitleCSL-RITA complex bound to DNA
Components
  • DNA (5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)-3')
  • DNA (5'-D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3')
  • Recombining binding protein suppressor of hairless
  • hRITA
KeywordsTRANSCRIPTION/DNA BINDING PROTEIN/DNA / Notch / RBPJ / TRANSCRIPTION-DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


determination of heart left/right asymmetry / blood vessel endothelial cell fate specification / positive regulation of ERBB signaling pathway / arterial endothelial cell fate commitment / blood vessel lumenization / regulation of generation of precursor metabolites and energy / club cell differentiation / regulation of timing of cell differentiation / positive regulation of ephrin receptor signaling pathway / pulmonary valve development ...determination of heart left/right asymmetry / blood vessel endothelial cell fate specification / positive regulation of ERBB signaling pathway / arterial endothelial cell fate commitment / blood vessel lumenization / regulation of generation of precursor metabolites and energy / club cell differentiation / regulation of timing of cell differentiation / positive regulation of ephrin receptor signaling pathway / pulmonary valve development / dorsal aorta morphogenesis / sebaceous gland development / endocardium morphogenesis / MAML1-RBP-Jkappa- ICN1 complex / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / auditory receptor cell fate commitment / positive regulation of transcription of Notch receptor target / secondary heart field specification / Notch-HLH transcription pathway / aortic valve development / positive regulation of cell proliferation involved in heart morphogenesis / epithelial to mesenchymal transition involved in endocardial cushion formation / epidermal cell fate specification / heart induction / cardiac left ventricle morphogenesis / pituitary gland development / endocardium development / negative regulation of smooth muscle cell migration / regulation of cell adhesion involved in heart morphogenesis / 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 / inflammatory response to antigenic stimulus / nuclear export / negative regulation of ossification / artery morphogenesis / negative regulation of cold-induced thermogenesis / labyrinthine layer blood vessel development / ventricular septum morphogenesis / heart looping / outflow tract morphogenesis / humoral immune response / negative regulation of smooth muscle cell apoptotic process / hemopoiesis / somatic stem cell population maintenance / epithelial to mesenchymal transition / negative regulation of Notch signaling pathway / negative regulation of cell differentiation / cell fate commitment / blood vessel remodeling / somitogenesis / positive regulation of cardiac muscle cell proliferation / keratinocyte differentiation / Notch signaling pathway / transcription repressor complex / neurogenesis / positive regulation of smooth muscle cell proliferation / B cell differentiation / tubulin binding / protein-DNA complex / neuron differentiation / positive regulation of canonical Wnt signaling pathway / regulation of cell population proliferation / negative regulation of neuron projection development / heart development / regulation of gene expression / angiogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / DNA-binding transcription factor binding / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / 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 cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / centrosome / positive regulation of DNA-templated transcription / protein-containing complex binding / nucleolus / 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
RBPJ-interacting and tubulin-associated protein 1 / RBPJ-interacting and tubulin associated protein / 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 ...RBPJ-interacting and tubulin-associated protein 1 / RBPJ-interacting and tubulin associated protein / 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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / p53-like transcription factor, DNA-binding / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
1,4-BUTANEDIOL / DNA / DNA (> 10) / Recombining binding protein suppressor of hairless / RBPJ-interacting and tubulin-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.094 Å
AuthorsTabaja, N.H. / Kovall, R.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA178974-02 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)T32CA117846-07 United States
CitationJournal: To Be Published
Title: CSL-RITA complex bound to DNA
Authors: Tabaja, N.H. / Kovall, R.A.
History
DepositionOct 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: DNA (5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)-3')
C: Recombining binding protein suppressor of hairless
R: hRITA
A: DNA (5'-D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,60630
Polymers58,7964
Non-polymers1,81026
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8840 Å2
ΔGint19 kcal/mol
Surface area25990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.788, 96.410, 96.711
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11C-701-

HOH

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Components

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DNA chain , 2 types, 2 molecules BA

#1: DNA chain DNA (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 / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (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 / Source: (synth.) synthetic construct (others)

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Protein / Protein/peptide , 2 types, 2 molecules CR

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


Mass: 47869.641 Da / Num. of mol.: 1 / Fragment: residues 53-474
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
#3: Protein/peptide hRITA


Mass: 1749.060 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q96K30*PLUS

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Non-polymers , 3 types, 187 molecules

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


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 277 K / Method: microbatch
Details: 0.1M Bis-Tris pH5.5, 0.2M Ammonium Acetate, 10% 1,4-butanediol, and 16% polyethylene glycol 3350
PH range: 5.5

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.094→50 Å / Num. obs: 42943 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 25.79 Å2 / Rmerge(I) obs: 0.074 / Χ2: 0.93 / Net I/av σ(I): 22.83 / Net I/σ(I): 7.6 / Num. measured all: 303810
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.094-2.145.50.53621020.86398.6
2.14-2.1860.51621070.87399.6
2.18-2.226.80.45721270.899100
2.22-2.267.20.41720970.924100
2.26-2.317.40.36521390.946100
2.31-2.377.40.33121250.951100
2.37-2.427.40.2921320.953100
2.42-2.497.40.26721180.939100
2.49-2.567.40.22421060.971100
2.56-2.657.40.1921290.966100
2.65-2.747.40.16821441.044100
2.74-2.857.40.14421521.088100
2.85-2.987.40.1221301.121100
2.98-3.147.30.10121321.149100
3.14-3.337.30.07921751.00799.9
3.33-3.597.20.06921370.92100
3.59-3.957.20.06221750.884100
3.95-4.5270.05521770.85100
4.52-5.770.04522260.58999.9
5.7-506.50.04623130.59899

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data collection
HKL-2000data scaling
PHASER2.5.3phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.094→40.827 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.25 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 1981 5.15 %
Rwork0.1978 --
obs0.1999 38480 89.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.094→40.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 609 118 161 4269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074249
X-RAY DIFFRACTIONf_angle_d1.2295822
X-RAY DIFFRACTIONf_dihedral_angle_d19.2421627
X-RAY DIFFRACTIONf_chiral_restr0.078637
X-RAY DIFFRACTIONf_plane_restr0.005635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0942-2.14660.2831730.19851389X-RAY DIFFRACTION48
2.1466-2.20460.2581980.20741872X-RAY DIFFRACTION65
2.2046-2.26950.28021190.21672195X-RAY DIFFRACTION77
2.2695-2.34270.26371320.21552451X-RAY DIFFRACTION86
2.3427-2.42640.29641400.22622699X-RAY DIFFRACTION93
2.4264-2.52360.29781490.22542730X-RAY DIFFRACTION95
2.5236-2.63840.26121530.23132786X-RAY DIFFRACTION97
2.6384-2.77750.28321540.23422819X-RAY DIFFRACTION98
2.7775-2.95140.29441590.23372843X-RAY DIFFRACTION98
2.9514-3.17920.25491590.21282872X-RAY DIFFRACTION99
3.1792-3.4990.24651580.20592888X-RAY DIFFRACTION99
3.499-4.0050.231590.18822927X-RAY DIFFRACTION99
4.005-5.04440.18631640.15312946X-RAY DIFFRACTION100
5.0444-40.83460.18521640.17473082X-RAY DIFFRACTION99

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