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- PDB-6py8: Crystal structure of the RBPJ-NOTCH1-NRARP ternary complex bound ... -

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Basic information

Entry
Database: PDB / ID: 6py8
TitleCrystal structure of the RBPJ-NOTCH1-NRARP ternary complex bound to DNA
Components
  • (DNA) x 2
  • Neurogenic locus notch homolog protein 1
  • Notch-regulated ankyrin repeat-containing protein
  • Recombining binding protein suppressor of hairless
KeywordsDNA BINDING PROTEIN/DNA / NOTCH1 / NRARP / RBPJ / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of Notch signaling pathway involved in somitogenesis / 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 / somite rostral/caudal axis specification / regulation of timing of cell differentiation / regulation of reproductive process ...negative regulation of Notch signaling pathway involved in somitogenesis / 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 / somite rostral/caudal axis specification / 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 / Defective LFNG causes SCDO3 / negative regulation of T cell differentiation / dorsal aorta morphogenesis / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / cardiac right ventricle formation / growth involved in heart morphogenesis / Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation / cell differentiation in spinal cord / retinal cone cell differentiation / venous endothelial cell differentiation / sebaceous gland development / arterial endothelial cell differentiation / cardiac chamber formation / epithelial cell fate commitment / negative regulation of pro-B cell differentiation / Pre-NOTCH Processing in the Endoplasmic Reticulum / negative regulation of inner ear auditory receptor cell differentiation / mitral valve formation / cell migration involved in endocardial cushion formation / glomerular mesangial cell development / negative regulation of photoreceptor cell differentiation / negative regulation of cell proliferation involved in heart valve morphogenesis / regulation of somitogenesis / inhibition of neuroepithelial cell differentiation / endocardium morphogenesis / atrioventricular node development / foregut morphogenesis / regulation of cell adhesion involved in heart morphogenesis / distal tubule development / MAML1-RBP-Jkappa- ICN1 complex / regulation of epithelial cell proliferation involved in prostate gland development / aortic valve development / auditory receptor cell fate commitment / positive regulation of aorta morphogenesis / negative regulation of endothelial cell chemotaxis / neuroendocrine cell differentiation / collecting duct development / negative regulation of extracellular matrix constituent secretion / positive regulation of transcription of Notch receptor target / cellular response to tumor cell / positive regulation of apoptotic process involved in morphogenesis / compartment pattern specification / vasculogenesis involved in coronary vascular morphogenesis / T-helper 17 type immune response / regulation of extracellular matrix assembly / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / cardiac ventricle morphogenesis / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / positive regulation of smooth muscle cell differentiation / cardiac left ventricle morphogenesis / mesenchymal cell development / epidermal cell fate specification / coronary vein morphogenesis / negative regulation of collagen biosynthetic process / cardiac vascular smooth muscle cell development / pituitary gland development / negative regulation of myotube differentiation / somatic stem cell division / left/right axis specification / NOTCH2 intracellular domain regulates transcription / negative regulation of cardiac muscle hypertrophy / negative regulation of cell adhesion molecule production / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / interleukin-17-mediated signaling pathway / positive regulation of endothelial cell differentiation / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / endocardium development / apoptotic process involved in embryonic digit morphogenesis / positive regulation of cardiac epithelial to mesenchymal transition / atrioventricular canal development / Pre-NOTCH Processing in Golgi / cardiac epithelial to mesenchymal transition / negative regulation of calcium ion-dependent exocytosis / cardiac muscle cell myoblast differentiation / cellular response to follicle-stimulating hormone stimulus / pericardium morphogenesis / cardiac atrium morphogenesis / negative regulation of catalytic activity / hair follicle maturation / neuronal stem cell population maintenance / tissue regeneration / regulation of stem cell proliferation / negative regulation of oligodendrocyte differentiation / myeloid dendritic cell differentiation
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 / Neurogenic locus notch homolog protein 1 / 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 / Domain of unknown function DUF3447 / Notch domain / Domain found in Notch and Lin-12 / EGF-like, conserved site / Human growth factor-like EGF / Calcium-binding EGF domain / Ankyrin repeat-containing domain / Ankyrin repeats (many copies) / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / p53-like transcription factor, DNA-binding / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Neurogenic locus notch homolog protein 1 / Recombining binding protein suppressor of hairless / Notch-regulated ankyrin repeat-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.75 Å
AuthorsJarrett, S.M. / Seegar, T.C.M. / Blacklow, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R35 CA220340 United States
CitationJournal: Sci.Signal. / Year: 2019
Title: Extension of the Notch intracellular domain ankyrin repeat stack by NRARP promotes feedback inhibition of Notch signaling.
Authors: Jarrett, S.M. / Seegar, T.C.M. / Andrews, M. / Adelmant, G. / Marto, J.A. / Aster, J.C. / Blacklow, S.C.
History
DepositionJul 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 2.0Sep 4, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Structure summary
Category: atom_site / cell ...atom_site / cell / computing / entity / entity_poly / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / struct_asym / struct_conf / struct_conn / struct_ref_seq / struct_sheet_range
Item: _cell.Z_PDB / _entity.pdbx_number_of_molecules ..._cell.Z_PDB / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_strand_id / _ndb_struct_na_base_pair.j_label_asym_id / _ndb_struct_na_base_pair_step.j_label_asym_id_1 / _ndb_struct_na_base_pair_step.j_label_asym_id_2 / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_percent_reflns_obs / _refine_hist.d_res_high / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.end_label_asym_id
Revision 2.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.3Oct 11, 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
B: Notch-regulated ankyrin repeat-containing protein
G: Notch-regulated ankyrin repeat-containing protein
A: DNA
X: DNA
D: DNA
Y: DNA
C: Recombining binding protein suppressor of hairless
E: Recombining binding protein suppressor of hairless
F: Neurogenic locus notch homolog protein 1
K: Neurogenic locus notch homolog protein 1


Theoretical massNumber of molelcules
Total (without water)226,37410
Polymers226,37410
Non-polymers00
Water0
1
B: Notch-regulated ankyrin repeat-containing protein
A: DNA
D: DNA
E: Recombining binding protein suppressor of hairless
F: Neurogenic locus notch homolog protein 1


Theoretical massNumber of molelcules
Total (without water)113,1875
Polymers113,1875
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-50 kcal/mol
Surface area41670 Å2
MethodPISA
2
G: Notch-regulated ankyrin repeat-containing protein
X: DNA
Y: DNA
C: Recombining binding protein suppressor of hairless
K: Neurogenic locus notch homolog protein 1


Theoretical massNumber of molelcules
Total (without water)113,1875
Polymers113,1875
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10100 Å2
ΔGint-50 kcal/mol
Surface area41140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.880, 103.650, 301.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Notch-regulated ankyrin repeat-containing protein


Mass: 12505.126 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRARP / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z6K4
#2: DNA chain DNA /


Mass: 5002.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA /


Mass: 4793.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Protein Recombining binding protein suppressor of hairless / CBF-1 / J kappa-recombination signal-binding protein / RBP-J kappa / RBP-JK / Renal carcinoma ...CBF-1 / J kappa-recombination signal-binding protein / RBP-J kappa / RBP-JK / Renal carcinoma antigen NY-REN-30


Mass: 50027.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBPJ, IGKJRB, IGKJRB1, RBPJK, RBPSUH / Production host: Escherichia coli (E. coli) / References: UniProt: Q06330
#5: Protein Neurogenic locus notch homolog protein 1 / hN1 / Translocation-associated notch protein TAN-1


Mass: 40859.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOTCH1, TAN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P46531

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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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 50 mM Hepes pH 6.8, 200 mM Sodium Fluoride, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.754→48.46 Å / Num. obs: 26271 / % possible obs: 99.17 % / Redundancy: 4.4 % / CC1/2: 0.998 / Net I/σ(I): 7.39
Reflection shellResolution: 3.754→3.888 Å / Num. unique obs: 2504 / CC1/2: 0.689

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata scaling
PHASERphasing
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F8X

2f8x


Resolution: 3.75→48.46 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 35.22
RfactorNum. reflection% reflection
Rfree0.315 1998 7.62 %
Rwork0.267 --
obs0.27 26212 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.75→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12005 1300 0 0 13305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213699
X-RAY DIFFRACTIONf_angle_d0.57318813
X-RAY DIFFRACTIONf_dihedral_angle_d12.3898045
X-RAY DIFFRACTIONf_chiral_restr0.042089
X-RAY DIFFRACTIONf_plane_restr0.0042246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7543-3.84820.41351360.36421651X-RAY DIFFRACTION96
3.8482-3.95220.37921390.34571698X-RAY DIFFRACTION100
3.9522-4.06840.38271400.31911688X-RAY DIFFRACTION100
4.0684-4.19970.33081430.30251737X-RAY DIFFRACTION100
4.1997-4.34970.36631400.28741684X-RAY DIFFRACTION100
4.3497-4.52370.35691400.28981710X-RAY DIFFRACTION99
4.5237-4.72950.28771430.26921720X-RAY DIFFRACTION100
4.7295-4.97860.33181410.25911718X-RAY DIFFRACTION100
4.9786-5.29020.32391440.26711734X-RAY DIFFRACTION100
5.2902-5.69810.37011440.27951746X-RAY DIFFRACTION100
5.6981-6.27040.3441410.28071719X-RAY DIFFRACTION100
6.2704-7.17540.34991470.28391765X-RAY DIFFRACTION100
7.1754-9.03090.26331460.22591789X-RAY DIFFRACTION100
9.0309-49.01250.23571540.21631855X-RAY DIFFRACTION98

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