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- PDB-7rte: X-ray structure of wild type RBPJ-L3MBTL3-DNA complex -

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Basic information

Entry
Database: PDB / ID: 7rte
TitleX-ray structure of wild type RBPJ-L3MBTL3-DNA complex
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')
  • Lethal(3)malignant brain tumor-like protein 3
  • Recombining binding protein suppressor of hairless
KeywordsDNA BINDING PROTEIN/DNA / Notch signaling / transcription / RBPJ / CSL / L3MBTL3 / 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 / methylation-dependent protein binding ...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 / methylation-dependent protein binding / positive regulation of ephrin receptor signaling pathway / secondary heart field specification / pulmonary valve development / positive regulation of cell proliferation involved in heart morphogenesis / dorsal aorta morphogenesis / sebaceous gland development / 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 / epithelial to mesenchymal transition involved in endocardial cushion formation / heart induction / granulocyte differentiation / cardiac left ventricle morphogenesis / epidermal cell fate specification / pituitary gland development / regulation of DNA methylation-dependent heterochromatin formation / endocardium development / atrioventricular canal development / cardiac muscle cell myoblast differentiation / hair follicle maturation / myeloid dendritic cell differentiation / ventricular trabecula myocardium morphogenesis / positive regulation of ubiquitin-dependent protein catabolic process / positive regulation of BMP signaling pathway / regulation of epithelial cell proliferation / inflammatory response to antigenic stimulus / negative regulation of ossification / negative regulation of cold-induced thermogenesis / labyrinthine layer blood vessel development / artery morphogenesis / ventricular septum morphogenesis / heart looping / outflow tract morphogenesis / erythrocyte maturation / somatic stem cell population maintenance / negative regulation of cell differentiation / humoral immune response / macrophage differentiation / hemopoiesis / 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 / Notch signaling pathway / 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 / chromatin organization / heart development / histone binding / 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 / sequence-specific DNA binding / transcription regulator complex / 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 / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
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 / 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 / Zinc finger, C2H2C-type / Zinc finger CCHHC-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat / SAM domain (Sterile alpha motif) / p53-like transcription factor, DNA-binding / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
beta-D-xylofuranose / DNA / DNA (> 10) / Recombining binding protein suppressor of hairless / Lethal(3)malignant brain tumor-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Synthetic DNA (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsHall, D.P. / Kovall, R.A. / Yuan, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5RO1CA178974 United States
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: The structure, binding and function of a Notch transcription complex involving RBPJ and the epigenetic reader protein L3MBTL3.
Authors: Hall, D. / Giaimo, B.D. / Park, S.S. / Hemmer, W. / Friedrich, T. / Ferrante, F. / Bartkuhn, M. / Yuan, Z. / Oswald, F. / Borggrefe, T. / Rual, J.F. / Kovall, R.A.
History
DepositionAug 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Source and taxonomy / Category: entity_src_gen / pdbx_entity_src_syn
Item: _entity_src_gen.gene_src_common_name / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._entity_src_gen.gene_src_common_name / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific
Revision 1.2Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 18, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Lethal(3)malignant brain tumor-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0429
Polymers58,6434
Non-polymers3985
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-18 kcal/mol
Surface area25090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.920, 96.930, 105.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules AB

#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.) Synthetic DNA (others)
#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.) Synthetic DNA (others)

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Protein / Protein/peptide / Sugars , 3 types, 3 molecules CD

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


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: Escadabiidae (arthropod) / References: UniProt: P31266
#4: Protein/peptide Lethal(3)malignant brain tumor-like protein 3 / H-l(3)mbt-like protein 3 / L(3)mbt-like protein 3 / L3mbt-like 3 / MBT-1


Mass: 1508.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96JM7
#6: Sugar ChemComp-XYZ / beta-D-xylofuranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C5H10O5
IdentifierTypeProgram
DXylfbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylofuranoseCOMMON NAMEGMML 1.0
b-D-XylfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 155 molecules

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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.97 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: MES monohydrate PIPES hexamminecobalt(III) chloride HEPES PEG 3350

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.056→39.459 Å / Num. obs: 43743 / % possible obs: 99.11 % / Redundancy: 5.6 % / CC1/2: 0.98 / Rmerge(I) obs: 0.105 / Net I/σ(I): 8
Reflection shellResolution: 2.056→2.1007 Å / Num. unique obs: 2546 / CC1/2: 0.68

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IAG

3iag


Resolution: 2.06→39.45 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2352 2190 5.01 %
Rwork0.1988 --
obs0.2006 43743 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→39.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3403 609 26 151 4189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084181
X-RAY DIFFRACTIONf_angle_d0.9655780
X-RAY DIFFRACTIONf_dihedral_angle_d22.361770
X-RAY DIFFRACTIONf_chiral_restr0.055646
X-RAY DIFFRACTIONf_plane_restr0.007633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.10.31041370.2942546X-RAY DIFFRACTION100
2.1-2.150.29531400.27162592X-RAY DIFFRACTION100
2.15-2.20.28471280.25042605X-RAY DIFFRACTION100
2.2-2.260.27031360.24712573X-RAY DIFFRACTION100
2.26-2.330.29111480.24572585X-RAY DIFFRACTION100
2.33-2.40.36071400.24072578X-RAY DIFFRACTION100
2.4-2.490.24621300.24032586X-RAY DIFFRACTION100
2.49-2.590.28861410.23832593X-RAY DIFFRACTION100
2.59-2.710.26951350.24222628X-RAY DIFFRACTION100
2.71-2.850.32561250.24642601X-RAY DIFFRACTION100
2.85-3.030.30141620.242594X-RAY DIFFRACTION100
3.03-3.260.21351050.21592612X-RAY DIFFRACTION99
3.26-3.590.24221380.20162622X-RAY DIFFRACTION99
3.59-4.110.20121450.1782584X-RAY DIFFRACTION98
4.11-5.180.17161380.14052603X-RAY DIFFRACTION97
5.18-39.450.19631420.15822651X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 6.9868 Å / Origin y: -8.8896 Å / Origin z: -18.9099 Å
111213212223313233
T0.3009 Å2-0.0051 Å2-0.0222 Å2-0.2715 Å20.0102 Å2--0.286 Å2
L1.2397 °20.1202 °2-0.5562 °2-0.3669 °20.0084 °2--0.5362 °2
S-0.0641 Å °0.067 Å °0.1126 Å °-0.0097 Å °0.0249 Å °0.0169 Å °0.1059 Å °-0.0877 Å °0 Å °
Refinement TLS groupSelection details: all

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