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- PDB-1yyh: Crystal structure of the human Notch 1 ankyrin domain -

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Basic information

Entry
Database: PDB / ID: 1yyh
TitleCrystal structure of the human Notch 1 ankyrin domain
ComponentsNotch 1, ankyrin domain
KeywordsCELL CYCLE / TRANSCRIPTION / ankyrin repeats / Notch 1
Function / homology
Function and homology information


Defective LFNG causes SCDO3 / 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 ...Defective LFNG causes SCDO3 / 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 / 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 / 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 / auditory receptor cell fate commitment / positive regulation of aorta morphogenesis / negative regulation of endothelial cell chemotaxis / atrioventricular node development / positive regulation of transcription of Notch receptor target / neuroendocrine cell differentiation / negative regulation of extracellular matrix constituent secretion / cellular response to tumor cell / collecting duct development / compartment pattern specification / positive regulation of apoptotic process involved in morphogenesis / vasculogenesis involved in coronary vascular morphogenesis / regulation of extracellular matrix assembly / T-helper 17 type immune response / endocardial cell differentiation / chemical synaptic transmission, postsynaptic / epithelial to mesenchymal transition involved in endocardial cushion formation / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / cardiac ventricle morphogenesis / positive regulation of smooth muscle cell differentiation / mesenchymal cell development / epidermal cell fate specification / glomerular mesangial cell development / negative regulation of myotube differentiation / coronary vein morphogenesis / cardiac left ventricle morphogenesis / cardiac vascular smooth muscle cell development / left/right axis specification / somatic stem cell division / negative regulation of cell adhesion molecule production / tissue regeneration / negative regulation of catalytic activity / interleukin-17-mediated signaling pathway / apoptotic process involved in embryonic digit morphogenesis / endocardium development / positive regulation of endothelial cell differentiation / positive regulation of cardiac epithelial to mesenchymal transition / Pre-NOTCH Processing in Golgi / cardiac epithelial to mesenchymal transition / negative regulation of collagen biosynthetic process / pericardium morphogenesis / cardiac atrium morphogenesis / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / negative regulation of cardiac muscle hypertrophy / cardiac muscle cell myoblast differentiation / cellular response to follicle-stimulating hormone stimulus / negative regulation of calcium ion-dependent exocytosis / neuronal stem cell population maintenance / calcium-ion regulated exocytosis / negative regulation of oligodendrocyte differentiation / positive regulation of astrocyte differentiation / pulmonary valve morphogenesis / heart trabecula morphogenesis / regulation of stem cell proliferation / coronary artery morphogenesis / luteolysis / prostate gland epithelium morphogenesis / negative regulation of biomineral tissue development / endoderm development / negative regulation of myoblast differentiation / negative regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion mediated by cadherin / ventricular trabecula myocardium morphogenesis / tube formation / positive regulation of BMP signaling pathway / astrocyte differentiation / positive regulation of keratinocyte differentiation / transcription regulator activator activity / negative regulation of stem cell differentiation / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / inflammatory response to antigenic stimulus / cardiac muscle tissue morphogenesis / positive regulation of Ras protein signal transduction
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 / Ankyrin repeats (many copies) / : / 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 1. / EGF-like domain signature 2. / 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 / Mainly Alpha
Similarity search - Domain/homology
Neurogenic locus notch homolog protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsEhebauer, M.T. / Chirgadze, D.Y. / Hayward, P. / Martinez-Arias, A. / Blundell, T.L.
CitationJournal: Biochem.J. / Year: 2005
Title: High-resolution crystal structure of the human Notch 1 ankyrin domain
Authors: Ehebauer, M.T. / Chirgadze, D.Y. / Hayward, P. / Martinez-Arias, A. / Blundell, T.L.
History
DepositionFeb 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.4Aug 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Notch 1, ankyrin domain
B: Notch 1, ankyrin domain


Theoretical massNumber of molelcules
Total (without water)55,5582
Polymers55,5582
Non-polymers00
Water9,674537
1
A: Notch 1, ankyrin domain


Theoretical massNumber of molelcules
Total (without water)27,7791
Polymers27,7791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Notch 1, ankyrin domain


Theoretical massNumber of molelcules
Total (without water)27,7791
Polymers27,7791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.840, 96.840, 108.996
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Cell settinghexagonal
Space group name H-MP65

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Components

#1: Protein Notch 1, ankyrin domain / Neurogenic locus notch homolog protein 1 / hN1 / Translocation-associated notch protein TAN-1


Mass: 27778.844 Da / Num. of mol.: 2 / Fragment: ankyrin domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOTCH1, TAN1 / Plasmid: pET41 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P46531
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.7 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium hydrogen phosphate, sodium chloride, imidazole, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 2005
RadiationMonochromator: DARESBURY / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.9→83.92 Å / Num. all: 44926 / Num. obs: 44926 / % possible obs: 98.5 % / Observed criterion σ(I): 2.5 / Redundancy: 3.6 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 12.4
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 12.4 / Num. unique all: 3138 / Rsym value: 0.385 / % possible all: 98.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OT8

1ot8


Resolution: 1.901→83.92 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.271 / SU ML: 0.068 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19264 2261 5 %RANDOM
Rwork0.16112 ---
all0.16272 44926 --
obs0.16272 42631 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.781 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20.36 Å20 Å2
2--0.72 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.901→83.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 0 537 3481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212984
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9454054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3675380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.89924.194155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90815499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8851530
X-RAY DIFFRACTIONr_chiral_restr0.1120.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022292
X-RAY DIFFRACTIONr_nbd_refined0.2070.21520
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22091
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2358
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.232
X-RAY DIFFRACTIONr_mcbond_it2.88851974
X-RAY DIFFRACTIONr_mcangle_it3.48763040
X-RAY DIFFRACTIONr_scbond_it4.01151112
X-RAY DIFFRACTIONr_scangle_it5.7797.51014
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 181 -
Rwork0.226 3138 -
obs-3138 98.72 %

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