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- PDB-7rti: X-ray structure of RBPJ-L3MBTL3(dT62)-DNA complex -

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Basic information

Entry
Database: PDB / ID: 7rti
TitleX-ray structure of RBPJ-L3MBTL3(dT62)-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 / 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 generation of precursor metabolites and energy / regulation of timing of cell differentiation / methylation-dependent protein binding / positive regulation of ephrin receptor signaling pathway ...determination of heart left/right asymmetry / 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 generation of precursor metabolites and energy / regulation of timing of cell differentiation / methylation-dependent protein binding / positive regulation of ephrin receptor signaling pathway / pulmonary valve development / dorsal aorta morphogenesis / sebaceous gland development / positive regulation of cell proliferation involved in heart morphogenesis / endocardium morphogenesis / MAML1-RBP-Jkappa- ICN1 complex / secondary heart field specification / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / auditory receptor cell fate commitment / aortic valve development / positive regulation of transcription of Notch receptor target / Notch-HLH transcription pathway / heart induction / epithelial to mesenchymal transition involved in endocardial cushion formation / epidermal cell fate specification / pituitary gland development / cardiac left ventricle morphogenesis / endocardium development / regulation of cell adhesion involved in heart morphogenesis / granulocyte differentiation / negative regulation of transcription initiation-coupled chromatin remodeling / atrioventricular canal development / hair follicle maturation / cardiac muscle cell myoblast differentiation / myeloid dendritic cell differentiation / ventricular trabecula myocardium morphogenesis / positive regulation of BMP signaling pathway / regulation of epithelial cell proliferation / inflammatory response to antigenic stimulus / positive regulation of ubiquitin-dependent protein catabolic process / negative regulation of ossification / negative regulation of cold-induced thermogenesis / artery morphogenesis / labyrinthine layer blood vessel development / ventricular septum morphogenesis / erythrocyte maturation / heart looping / outflow tract morphogenesis / humoral immune response / hemopoiesis / macrophage differentiation / blood vessel remodeling / negative regulation of cell differentiation / somatic stem cell population maintenance / epithelial to mesenchymal transition / 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 / positive regulation of epithelial cell proliferation / epithelial cell proliferation / stem cell proliferation / neuron differentiation / positive regulation of canonical Wnt signaling pathway / chromatin organization / heart development / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / histone binding / cell differentiation / cell population proliferation / defense response to bacterium / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
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
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: 2.05 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

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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)58,6676
Polymers58,5424
Non-polymers1242
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-20 kcal/mol
Surface area25240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.790, 97.080, 105.540
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 , 2 types, 2 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: Escherichia coli (E. coli) / 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: 1407.675 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: delta T62 / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96JM7

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Non-polymers , 2 types, 147 molecules

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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 58.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: ammonium fluoride PEG 3350

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 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: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.05→97.08 Å / Num. obs: 43800 / % possible obs: 98.74 % / Redundancy: 6.3 % / CC1/2: 0.997 / Net I/σ(I): 10.6
Reflection shellResolution: 2.051→2.0956 Å / Num. unique obs: 2556 / CC1/2: 0.78

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Processing

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

3iag


Resolution: 2.05→71.45 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2228 2178 4.97 %
Rwork0.1882 --
obs0.1898 43800 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→71.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3408 609 8 145 4170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084170
X-RAY DIFFRACTIONf_angle_d0.9365764
X-RAY DIFFRACTIONf_dihedral_angle_d21.422763
X-RAY DIFFRACTIONf_chiral_restr0.054639
X-RAY DIFFRACTIONf_plane_restr0.008633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.30591380.26632556X-RAY DIFFRACTION100
2.1-2.140.29671390.25092609X-RAY DIFFRACTION100
2.14-2.20.26691310.24352596X-RAY DIFFRACTION100
2.2-2.260.23611570.23112563X-RAY DIFFRACTION100
2.26-2.320.30741430.23542560X-RAY DIFFRACTION99
2.32-2.40.3061430.24252537X-RAY DIFFRACTION98
2.4-2.480.23411400.24082502X-RAY DIFFRACTION97
2.48-2.580.30251250.2342518X-RAY DIFFRACTION97
2.58-2.70.26911460.22372627X-RAY DIFFRACTION100
2.7-2.840.26041290.23072615X-RAY DIFFRACTION100
2.84-3.020.24981200.21722633X-RAY DIFFRACTION99
3.02-3.260.22191140.21262635X-RAY DIFFRACTION99
3.26-3.580.22121450.18312586X-RAY DIFFRACTION98
3.58-4.10.18731140.16572636X-RAY DIFFRACTION98
4.1-5.170.17381490.13522679X-RAY DIFFRACTION100
5.17-71.450.18411450.14752770X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1681-0.64560.20080.5594-0.08021.43950.05430.0164-0.04970.0606-0.1958-0.33620.25780.3351-0.00760.36380.04650.01130.29120.04580.496331.0638-16.5721-28.09
20.7563-0.2519-0.5260.8303-0.28951.49940.1245-0.1449-0.1601-0.1047-0.3428-0.39790.08010.3483-0.00060.38460.06-0.03210.30180.06040.412833.2164-10.8901-26.0853
31.28840.5042-0.16480.28290.19340.8365-0.1668-0.05530.09690.02210.02320.04740.1484-0.0643-0.00020.28680.0064-0.01930.23020.03630.26182.3872-5.1376-6.9081
41.04250.52-0.20891.2260.96831.64510.029-0.06720.4955-0.05440.00070.0164-0.1990.1373-0.00010.372-0.00340.00530.30060.00320.34687.4784.7032-6.1636
50.6842-0.0639-0.48410.63690.52192.1061-0.0458-0.05580.09340.03740.0328-0.00330.22080.0326-0.00020.2646-0.0035-0.00740.24650.02870.252811.9735-8.47-20.0859
61.4820.0169-0.56242.16430.07393.1883-0.09770.32430.0765-0.18430.05440.08690.2321-0.2277-0.00010.2993-0.0528-0.0480.41570.01770.27786.0573-10.1447-40.2711
70.89590.135-0.67720.2413-0.39570.0779-0.1012-0.00640.0449-0.042-0.05010.09210.029-0.0104-0.00060.3101-0.02360.0330.3416-0.05090.2882-4.9612-12.3127-3.2813
81.21991.22710.15171.84530.39980.4347-0.0093-0.21520.09160.0844-0.13070.32110.1112-0.0349-0.02290.2676-0.03970.05090.3211-0.06770.4019-19.3818-14.21450.2451
90.1167-0.1094-0.19430.63880.4350.2951-0.45920.64470.06030.02930.07780.53640.4054-0.6029-0.04440.38090.0404-0.08080.65410.11970.5212-3.5329-0.6782-38.9149
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )
2X-RAY DIFFRACTION2chain 'B' and (resid 16 through 30 )
3X-RAY DIFFRACTION3chain 'C' and (resid 52 through 97 )
4X-RAY DIFFRACTION4chain 'C' and (resid 98 through 155 )
5X-RAY DIFFRACTION5chain 'C' and (resid 156 through 245 )
6X-RAY DIFFRACTION6chain 'C' and (resid 246 through 354 )
7X-RAY DIFFRACTION7chain 'C' and (resid 355 through 410 )
8X-RAY DIFFRACTION8chain 'C' and (resid 411 through 473 )
9X-RAY DIFFRACTION9chain 'D' and (resid 57 through 69 )

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