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- PDB-2vj2: Human Jagged-1, domains DSL and EGFs1-3 -

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Basic information

Entry
Database: PDB / ID: 2vj2
TitleHuman Jagged-1, domains DSL and EGFs1-3
ComponentsJAGGED-1
KeywordsPROTEIN BINDING / SIGNALLING / POLYMORPHISM / GLYCOPROTEIN / EXTRACELLULAR / DEVELOPMENTAL PROTEIN / NOTCH SIGNALING PATHWAY / EGF / DSL / NOTCH / JAGGED / CALCIUM / MEMBRANE / PROTEIN-BINDING / TRANSMEMBRANE / EGF-LIKE DOMAIN / DISEASE MUTATION
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 / 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
Similarity search - Domain/homology
D-MALATE / Protein jagged-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.5 Å
AuthorsJohnson, S. / Cordle, J. / Tay, J.Z. / Roversi, P. / Handford, P.A. / Lea, S.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: A Conserved Face of the Jagged/Serrate Dsl Domain is Involved in Notch Trans-Activation and Cis-Inhibition.
Authors: Cordle, J. / Johnson, S. / Tay, J.Z. / Roversi, P. / Wilkin, M.B. / De Madrid, B.H. / Shimizu, H. / Jensen, S. / Whiteman, P. / Jin, B. / Redfield, C. / Baron, M. / Lea, S.M. / Handford, P.A.
History
DepositionDec 6, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: JAGGED-1
B: JAGGED-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7963
Polymers37,6622
Non-polymers1341
Water3,747208
1
A: JAGGED-1


Theoretical massNumber of molelcules
Total (without water)18,8311
Polymers18,8311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: JAGGED-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9652
Polymers18,8311
Non-polymers1341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.000, 102.300, 62.700
Angle α, β, γ (deg.)90.00, 114.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2028-

HOH

21B-2067-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.449, -0.006, -0.893), (-0.065, -0.998, -0.026), (-0.891, 0.07, -0.449)
Vector: 28.04469, 134.20255, 37.42754)

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Components

#1: Protein JAGGED-1 / JAGGED1 / HJ1 / CD339 ANTIGEN / JAGGED-1


Mass: 18831.086 Da / Num. of mol.: 2 / Fragment: DSL DOMAIN AND EGFS1-3, RESIDUES 185-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM554 / References: UniProt: P78504
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST 18 RESIDUES ARE FROM THE N-TERMINAL HIS-TAG ENCODED BY THE VECTOR

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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: 2.5 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 7 / Details: 8.5% (W/V) PEG4000, 100MM IMIDAZOLE -MALATE, PH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→57.1 Å / Num. obs: 11962 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.1
Reflection shellResolution: 2.5→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.3 / % possible all: 98.6

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Processing

Software
NameVersionClassification
BUSTER-TNTmodel building
SCALAdata scaling
autoSHARPphasing
SHARP-SOLOMONphasing
DMphasing
BUSTER-TNTphasing
TNT5.6.1refinement
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.5→48.5 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: BUSTER-TNT-GELLY 2.1.1 E. BLANC, P. ROVERSI, C. VONRHEIN, C. FLENSBURG, S. M. LEA AND G.BRICOGNE
RfactorNum. reflection% reflectionSelection details
Rfree0.239 584 5 %RANDOM
Rwork0.22 ---
all0.221 ---
obs0.221 11961 --
Solvent computationSolvent model: BABINET SCALING / Bsol: 131 Å2 / ksol: 0.35 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2299 0 9 208 2516
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00724032
X-RAY DIFFRACTIONt_angle_deg0.71632442
X-RAY DIFFRACTIONt_dihedral_angle_d16.74510
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.001722
X-RAY DIFFRACTIONt_gen_planes0.033565
X-RAY DIFFRACTIONt_it1.289240320
X-RAY DIFFRACTIONt_nbd0.11655
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact

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