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- PDB-2he0: Crystal structure of a human Notch1 ankyrin domain mutant -

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Basic information

Entry
Database: PDB / ID: 2he0
TitleCrystal structure of a human Notch1 ankyrin domain mutant
ComponentsNotch1 preproprotein variant
KeywordsSIGNALING PROTEIN / Notch / Ankyrin / signalling
Function / homology
Function and homology information


Defective LFNG causes SCDO3 / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / growth involved in heart morphogenesis / regulation of cardioblast proliferation / mesenchymal cell development / cell differentiation in spinal cord / venous endothelial cell differentiation / arterial endothelial cell differentiation / collecting duct development ...Defective LFNG causes SCDO3 / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / growth involved in heart morphogenesis / regulation of cardioblast proliferation / mesenchymal cell development / cell differentiation in spinal cord / venous endothelial cell differentiation / arterial endothelial cell differentiation / collecting duct development / cell migration involved in endocardial cushion formation / negative regulation of pro-B cell differentiation / Pre-NOTCH Processing in the Endoplasmic Reticulum / mitral valve formation / : / endocardium morphogenesis / distal tubule development / MAML1-RBP-Jkappa- ICN1 complex / cardiac chamber formation / cardiac atrium morphogenesis / negative regulation of endothelial cell chemotaxis / atrioventricular node development / cardiac ventricle morphogenesis / positive regulation of transcription of Notch receptor target / pericardium morphogenesis / cellular response to tumor cell / positive regulation of smooth muscle cell differentiation / glomerular mesangial cell development / vasculogenesis involved in coronary vascular morphogenesis / negative regulation of extracellular matrix constituent secretion / regulation of extracellular matrix assembly / positive regulation of apoptotic process involved in morphogenesis / chemical synaptic transmission, postsynaptic / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / left/right axis specification / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / T-helper 17 type immune response / positive regulation of endothelial cell differentiation / cardiac left ventricle morphogenesis / coronary vein morphogenesis / negative regulation of myotube differentiation / cardiac vascular smooth muscle cell development / endocardium development / neuronal stem cell population maintenance / positive regulation of astrocyte differentiation / negative regulation of cell adhesion molecule production / cardiac muscle cell myoblast differentiation / tissue regeneration / positive regulation of cardiac epithelial to mesenchymal transition / negative regulation of oligodendrocyte differentiation / cardiac epithelial to mesenchymal transition / heart trabecula morphogenesis / regulation of cell adhesion involved in heart morphogenesis / interleukin-17-mediated signaling pathway / Pre-NOTCH Processing in Golgi / negative regulation of catalytic activity / negative regulation of myoblast differentiation / negative regulation of collagen biosynthetic process / cellular response to follicle-stimulating hormone stimulus / negative regulation of cardiac muscle hypertrophy / negative regulation of stem cell differentiation / luteolysis / pulmonary valve morphogenesis / tube formation / determination of left/right symmetry / cardiac muscle tissue morphogenesis / coronary artery morphogenesis / negative regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion mediated by cadherin / ventricular trabecula myocardium morphogenesis / negative regulation of ossification / negative regulation of biomineral tissue development / astrocyte differentiation / positive regulation of BMP signaling pathway / transcription regulator activator activity / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of Ras protein signal transduction / oligodendrocyte differentiation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / Notch binding / atrioventricular valve morphogenesis / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of NFE2L2 gene expression / aortic valve morphogenesis / positive regulation of neuroblast proliferation / negative regulation of cold-induced thermogenesis / NOTCH3 Intracellular Domain Regulates Transcription / negative regulation of neuron differentiation / endocardial cushion morphogenesis / negative regulation of glial cell proliferation / NFE2L2 regulating tumorigenic genes / ventricular septum morphogenesis / response to muramyl dipeptide / cardiac septum morphogenesis / Notch-HLH transcription pathway / heart looping / Formation of paraxial mesoderm / Somitogenesis
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 (Lin-12/Notch) repeat profile. / LNR domain / Notch domain / Domain found in Notch and Lin-12 / EGF-like, conserved site / Human growth factor-like EGF / Ankyrin repeat-containing domain / : / Calcium-binding EGF domain / Ankyrin repeats (many copies) / 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 repeat profile. / Ankyrin repeats (3 copies) / 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: 1.9 Å
AuthorsGupta, D. / Ehebauer, M.T. / Chirgadze, D.Y. / Martinez Arias, A. / Blundell, T.L.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a human Notch1 ankyrin domain mutant
Authors: Gupta, D. / Ehebauer, M.T. / Chirgadze, D.Y. / Martinez Arias, A. / Blundell, T.L.
History
DepositionJun 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Notch1 preproprotein variant
B: Notch1 preproprotein variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3313
Polymers55,2692
Non-polymers621
Water7,494416
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.982, 96.982, 108.719
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Notch1 preproprotein variant / Human Notch ankyrin domain mutant


Mass: 27634.691 Da / Num. of mol.: 2 / Fragment: Ankyrin Domain, residues 1873-2115 / Mutation: E58A, R66A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Notch 1 / Plasmid: pET41a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P46531
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 3.26 Å3/Da / Density % sol: 62.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.55M Sodium/Potassium Tartrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9769 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9769 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 45594 / Num. obs: 45547 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 10.7 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 10.6
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.488 / Rsym value: 0.488 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YYH

1yyh


Resolution: 1.9→48.51 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.961 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23094 2297 5 %RANDOM
Rwork0.18777 ---
all0.18998 45547 --
obs0.18998 43201 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.288 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2969 0 4 416 3389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213017
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9414107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6595398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.11224.276152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52415489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9291528
X-RAY DIFFRACTIONr_chiral_restr0.1150.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022328
X-RAY DIFFRACTIONr_nbd_refined0.2320.21572
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22105
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.2319
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3250.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3380.241
X-RAY DIFFRACTIONr_mcbond_it3.34152013
X-RAY DIFFRACTIONr_mcangle_it3.97363102
X-RAY DIFFRACTIONr_scbond_it4.32951103
X-RAY DIFFRACTIONr_scangle_it5.6777.51001
LS refinement shellResolution: 1.901→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 180 -
Rwork0.252 3161 -
obs-3341 99.82 %

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