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- PDB-2kb9: Human Jagged-1, exon 6 -

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Basic information

Entry
Database: PDB / ID: 2kb9
TitleHuman Jagged-1, exon 6
ComponentsJagged-1
KeywordsPROTEIN BINDING / notch signaling / EGF / Calcium / Developmental protein / Disease mutation / EGF-like domain / Glycoprotein / Membrane / Notch signaling pathway / Polymorphism / Transmembrane
Function / homology
Function and homology information


endocardial cushion cell development / loop of Henle development / ciliary body morphogenesis / regulation of reproductive process / pulmonary artery morphogenesis / cardiac neural crest cell development involved in outflow tract morphogenesis / podocyte development / negative regulation of endothelial cell differentiation / morphogenesis of an epithelial sheet / nephron development ...endocardial cushion cell development / loop of Henle development / ciliary body morphogenesis / regulation of reproductive process / pulmonary artery morphogenesis / cardiac neural crest cell development involved in outflow tract morphogenesis / podocyte development / negative regulation of endothelial cell differentiation / morphogenesis of an epithelial sheet / nephron development / positive regulation of myeloid cell differentiation / Nephron development / cardiac right ventricle morphogenesis / inhibition of neuroepithelial cell differentiation / distal tubule development / neuroendocrine cell differentiation / aorta morphogenesis / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / positive regulation of cardiac epithelial to mesenchymal transition / NOTCH4 Activation and Transmission of Signal to the Nucleus / inner ear auditory receptor cell differentiation / T cell mediated immunity / endothelial cell differentiation / neuronal stem cell population maintenance / pulmonary valve morphogenesis / cell fate determination / negative regulation of stem cell differentiation / regulation of epithelial cell proliferation / aortic valve morphogenesis / Notch binding / myoblast differentiation / RUNX3 regulates NOTCH signaling / negative regulation of cell-matrix adhesion / negative regulation of cell-cell adhesion / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / cardiac septum morphogenesis / response to muramyl dipeptide / hemopoiesis / negative regulation of neuron differentiation / RAC3 GTPase cycle / blood vessel remodeling / positive regulation of osteoblast differentiation / keratinocyte differentiation / Notch signaling pathway / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / RAC1 GTPase cycle / Activated NOTCH1 Transmits Signal to the Nucleus / negative regulation of cell migration / NOTCH3 Activation and Transmission of Signal to the Nucleus / adherens junction / growth factor activity / phospholipid binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nervous system development / regulation of cell population proliferation / angiogenesis / molecular adaptor activity / apical plasma membrane / calcium ion binding / structural molecule activity / positive regulation of transcription by RNA polymerase II / extracellular region / membrane / plasma membrane
Similarity search - Function
Jagged/Serrate protein / Delta-like/Jagged, EGF-like domain / Delta/Serrate/lag-2 (DSL) protein / Notch ligand, N-terminal domain / Delta serrate ligand / N terminus of Notch ligand C2-like domain / DSL domain profile. / delta serrate ligand / EGF-like, conserved site / Human growth factor-like EGF ...Jagged/Serrate protein / Delta-like/Jagged, EGF-like domain / Delta/Serrate/lag-2 (DSL) protein / Notch ligand, N-terminal domain / Delta serrate ligand / N terminus of Notch ligand C2-like domain / DSL domain profile. / delta serrate ligand / EGF-like, conserved site / Human growth factor-like EGF / von Willebrand factor (vWF) type C domain / von Willebrand factor (vWF) type C domain / VWFC domain / : / Calcium-binding EGF domain / Laminin / Laminin / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Mainly Beta
Similarity search - Domain/homology
MethodSOLUTION NMR / torsion angle dynamics
Model detailsHuman Jagged-1, residues 252-295; includes the C-terminal part of EGF1 and the entire EGF2
AuthorsPintar, A. / Guarnaccia, C. / Pongor, S.
Citation
Journal: Bmc Struct.Biol. / Year: 2009
Title: Exon 6 of human JAG1 encodes a conserved structural unit
Authors: Pintar, A. / Guarnaccia, C. / Dhir, S. / Pongor, S.
#1: Journal: FEBS Lett. / Year: 2004
Title: Exon 6 of human Jagged-1 encodes an autonomously folding unit
Authors: Guarnaccia, C. / Pintar, A. / Pongor, S.
History
DepositionNov 24, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Jagged-1


Theoretical massNumber of molelcules
Total (without water)5,0491
Polymers5,0491
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Jagged-1 / Jagged1 / hJ1


Mass: 5048.784 Da / Num. of mol.: 1 / Fragment: residues 252-295 / Source method: obtained synthetically
Details: The protein is naturally found in Homo sapiens (human). The protein includes the C-terminal part of the EGF1 domain and the entire EGF2 domain.
References: UniProt: P78504

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1422D 1H-1H COSY
1522D 1H-1H TOCSY
1622D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM protein, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM protein, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.5 mMentity1
0.5 mMentity2
Sample conditionspH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR softwareName: CYANA / Version: 2.1 / Developer: Guntert P. / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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