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- PDB-1ymp: The Crystal Structure of a Partial Mouse Notch-1 Ankyrin Domain: ... -

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Basic information

Entry
Database: PDB / ID: 1ymp
TitleThe Crystal Structure of a Partial Mouse Notch-1 Ankyrin Domain: Repeats 4 Through 7 Preserve an Ankyrin Fold
ComponentsNotch 1 protein
KeywordsTRANSCRIPTION / ankyrin repeats / helix-turn-helix
Function / homology
Function and homology information


Notch signaling involved in heart development / Pre-NOTCH Processing in Golgi / regulation of cardioblast proliferation / regulation of inner ear auditory receptor cell differentiation / positive regulation of ephrin receptor signaling pathway / positive regulation of glial cell differentiation / osteoblast fate commitment / venous blood vessel morphogenesis / Activated NOTCH1 Transmits Signal to the Nucleus / coronary sinus valve morphogenesis ...Notch signaling involved in heart development / Pre-NOTCH Processing in Golgi / regulation of cardioblast proliferation / regulation of inner ear auditory receptor cell differentiation / positive regulation of ephrin receptor signaling pathway / positive regulation of glial cell differentiation / osteoblast fate commitment / venous blood vessel morphogenesis / Activated NOTCH1 Transmits Signal to the Nucleus / 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 / venous endothelial cell differentiation / retinal cone cell differentiation / arterial endothelial cell differentiation / epithelial cell fate commitment / negative regulation of pro-B cell differentiation / 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 / endocardium morphogenesis / foregut morphogenesis / regulation of cell adhesion involved in heart morphogenesis / distal tubule development / inhibition of neuroepithelial cell differentiation / MAML1-RBP-Jkappa- ICN1 complex / regulation of epithelial cell proliferation involved in prostate gland development / cardiac chamber formation / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / auditory receptor cell fate commitment / positive regulation of aorta morphogenesis / positive regulation of viral transcription / negative regulation of endothelial cell chemotaxis / atrioventricular node development / positive regulation of transcription of Notch receptor target / neuroendocrine cell differentiation / collecting duct development / negative regulation of extracellular matrix constituent secretion / cellular response to tumor cell / Notch-HLH transcription pathway / positive regulation of apoptotic process involved in morphogenesis / compartment pattern specification / vasculogenesis involved in coronary vascular morphogenesis / T-helper 17 type immune response / endocardial cushion development / regulation of extracellular matrix assembly / chemical synaptic transmission, postsynaptic / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / cardiac ventricle morphogenesis / positive regulation of smooth muscle cell differentiation / cardiac left ventricle morphogenesis / epidermal cell fate specification / mesenchymal cell development / negative regulation of collagen biosynthetic process / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / regulation of Notch signaling pathway / negative regulation of myotube differentiation / left/right axis specification / somatic stem cell division / negative regulation of cell adhesion molecule production / negative regulation of cardiac muscle hypertrophy / interleukin-17-mediated signaling pathway / positive regulation of endothelial cell differentiation / apoptotic process involved in embryonic digit morphogenesis / endocardium development / positive regulation of cardiac epithelial to mesenchymal transition / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / cardiac epithelial to mesenchymal transition / glial cell differentiation / neuron fate commitment / negative regulation of catalytic activity / pericardium morphogenesis / cardiac atrium morphogenesis / cardiac muscle cell myoblast differentiation / negative regulation of calcium ion-dependent exocytosis / cellular response to follicle-stimulating hormone stimulus / neuronal stem cell population maintenance / tissue regeneration / calcium-ion regulated exocytosis / pulmonary valve morphogenesis / negative regulation of oligodendrocyte differentiation / positive regulation of astrocyte differentiation / negative regulation of biomineral tissue development / regulation of stem cell proliferation / heart trabecula morphogenesis / coronary artery morphogenesis / luteolysis / negative regulation of cell-cell adhesion mediated by cadherin / endoderm development / prostate gland epithelium morphogenesis
Similarity search - Function
: / 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 ...: / 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 domain / LNR (Lin-12/Notch) repeat profile. / 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 / 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. / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Neurogenic locus notch homolog protein 1 / Neurogenic locus notch homolog protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLubman, O.Y. / Kopan, R. / Waksman, G. / Korolev, S.
CitationJournal: Protein Sci. / Year: 2005
Title: The crystal structure of a partial mouse Notch-1 ankyrin domain: repeats 4 through 7 preserve an ankyrin fold.
Authors: Lubman, O.Y. / Kopan, R. / Waksman, G. / Korolev, S.
History
DepositionJan 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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
A: Notch 1 protein
B: Notch 1 protein


Theoretical massNumber of molelcules
Total (without water)30,1562
Polymers30,1562
Non-polymers00
Water2,684149
1
A: Notch 1 protein


Theoretical massNumber of molelcules
Total (without water)15,0781
Polymers15,0781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Notch 1 protein


Theoretical massNumber of molelcules
Total (without water)15,0781
Polymers15,0781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.789, 75.789, 45.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Detailsbiological assembly is a monomer

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Components

#1: Protein Notch 1 protein


Mass: 15077.961 Da / Num. of mol.: 2 / Fragment: ankryin repeats 3.5-7 (residues 1971-2105)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Notch1 / Plasmid: pProEX HTc / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q07008, UniProt: Q01705*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 10000, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 14979 / % possible obs: 85.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.043 / Rsym value: 0.047
Reflection shellResolution: 2.2→2.34 Å / % possible all: 85.6

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.516 / Packing: 0.515
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Rotation3.5 Å15 Åfast direct97.4 0
Translation4 Å15 Ågeneral: ! target for PC-refinement= e2e298.7 0

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Processing

Software
NameVersionClassificationNB
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1N0R

1n0r


Resolution: 2.2→21.88 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: refined as perfect merohedral twin using CNS scripts
RfactorNum. reflection% reflectionSelection details
Rfree0.309 549 3.7 %random
Rwork0.206 ---
obs-11012 73.6 %-
Displacement parametersBiso mean: 73.912 Å2
Baniso -1Baniso -2Baniso -3
1--0.323 Å23.078 Å20 Å2
2---0.323 Å20 Å2
3---0.645 Å2
Refinement stepCycle: LAST / Resolution: 2.2→21.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 0 149 2098
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.69

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