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- PDB-4d0f: Human Notch1 EGF domains 11-13 mutant T466A -

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Basic information

Entry
Database: PDB / ID: 4d0f
TitleHuman Notch1 EGF domains 11-13 mutant T466A
ComponentsNEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1
KeywordsTRANSCRIPTION / METAL-BINDING / TRANSMEMBRANE / DEVELOPMENTAL / PROTEIN / NOTCH SIGNALING PATHWAY / DIFFERENTIATION / PHOSPHORYLATION / EGF-LIKE DOMAIN / REGULATION / RECEPTOR / ACTIVATOR / ANK REPEAT / SIGNALLING / GLYCOPROTEIN / EXTRACELLULAR / JAGGED / NUCLEUS / MEMBRANE
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 / retinal cone cell differentiation / venous endothelial 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 / retinal cone cell differentiation / venous endothelial cell differentiation / arterial endothelial cell differentiation / cardiac chamber formation / 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 / glomerular mesangial cell development / negative regulation of photoreceptor cell differentiation / negative regulation of cell proliferation involved in heart valve morphogenesis / regulation of somitogenesis / inhibition of neuroepithelial cell differentiation / endocardium morphogenesis / atrioventricular node development / foregut morphogenesis / regulation of cell adhesion involved in heart morphogenesis / distal tubule development / MAML1-RBP-Jkappa- ICN1 complex / regulation of epithelial cell proliferation involved in prostate gland development / auditory receptor cell fate commitment / positive regulation of aorta morphogenesis / negative regulation of endothelial cell chemotaxis / neuroendocrine cell differentiation / collecting duct development / negative regulation of extracellular matrix constituent secretion / positive regulation of transcription of Notch receptor target / cellular response to tumor cell / positive regulation of apoptotic process involved in morphogenesis / compartment pattern specification / vasculogenesis involved in coronary vascular morphogenesis / T-helper 17 type immune response / regulation of extracellular matrix assembly / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / cardiac ventricle morphogenesis / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / positive regulation of smooth muscle cell differentiation / cardiac left ventricle morphogenesis / mesenchymal cell development / epidermal cell fate specification / coronary vein morphogenesis / negative regulation of collagen biosynthetic process / cardiac vascular smooth muscle cell development / negative regulation of myotube differentiation / somatic stem cell division / left/right axis specification / negative regulation of cardiac muscle hypertrophy / negative regulation of cell adhesion molecule production / interleukin-17-mediated signaling pathway / positive regulation of endothelial cell differentiation / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / endocardium development / apoptotic process involved in embryonic digit morphogenesis / positive regulation of cardiac epithelial to mesenchymal transition / Pre-NOTCH Processing in Golgi / cardiac epithelial to mesenchymal transition / negative regulation of calcium ion-dependent exocytosis / cardiac muscle cell myoblast differentiation / cellular response to follicle-stimulating hormone stimulus / pericardium morphogenesis / cardiac atrium morphogenesis / negative regulation of catalytic activity / neuronal stem cell population maintenance / tissue regeneration / regulation of stem cell proliferation / negative regulation of oligodendrocyte differentiation / positive regulation of astrocyte differentiation / calcium-ion regulated exocytosis / pulmonary valve morphogenesis / heart trabecula morphogenesis / negative regulation of biomineral tissue development / endoderm development / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / prostate gland epithelium morphogenesis / luteolysis / cardiac muscle tissue morphogenesis / ventricular trabecula myocardium morphogenesis / negative regulation of myoblast differentiation / negative regulation of cell migration involved in sprouting angiogenesis / transcription regulator activator activity / positive regulation of BMP signaling pathway / tube formation / negative regulation of stem cell differentiation / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of keratinocyte differentiation / astrocyte differentiation / inflammatory response to antigenic stimulus / positive regulation of Ras protein signal transduction / negative regulation of ossification
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 / NODP ...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 / Calcium-binding EGF domain / Ankyrin repeats (many copies) / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / 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 / Ankyrin repeat-containing domain superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Neurogenic locus notch homolog protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTaylor, P. / Takeuchi, H. / Sheppard, D. / Chillakuri, C. / Lea, S.M. / Haltiwanger, R.S. / Handford, P.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Fringe-Mediated Extension of O-Linked Fucose in the Ligand-Binding Region of Notch1 Increases Binding to Mammalian Notch Ligands.
Authors: Taylor, P. / Takeuchi, H. / Sheppard, D. / Chillakuri, C. / Lea, S.M. / Haltiwanger, R.S. / Handford, P.A.
History
DepositionApr 25, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Atomic model
Revision 1.2Jun 4, 2014Group: Database references
Revision 1.3Feb 7, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0105
Polymers14,8281
Non-polymers1824
Water23413
1
A: NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1
hetero molecules

A: NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,02010
Polymers29,6552
Non-polymers3658
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
Buried area1080 Å2
ΔGint-35.7 kcal/mol
Surface area16620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.620, 62.620, 126.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1 / NOTCH 1 / HN1 / TRANSLOCATION-ASSOCIATED NOTCH PROTEIN TAN-1 / HUMAN NOTCH


Mass: 14827.578 Da / Num. of mol.: 1 / Fragment: EGF 11-13 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P46531
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.42 Å3/Da / Density % sol: 49.23 % / Description: NONE
Crystal growpH: 4.5 / Details: pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.75
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Feb 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.75 Å / Relative weight: 1
ReflectionResolution: 2.8→63.3 Å / Num. obs: 3956 / % possible obs: 99 % / Redundancy: 5.5 % / Biso Wilson estimate: 55.53 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.6
Reflection shellResolution: 2.8→3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VJ3

2vj3


Resolution: 2.8→41.19 Å / Cor.coef. Fo:Fc: 0.9171 / Cor.coef. Fo:Fc free: 0.8721 / SU R Cruickshank DPI: 2.048 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.384 / SU Rfree Cruickshank DPI: 0.363
RfactorNum. reflection% reflectionSelection details
Rfree0.2645 177 4.47 %RANDOM
Rwork0.2229 ---
obs0.2247 3956 98.6 %-
Displacement parametersBiso mean: 79.48 Å2
Baniso -1Baniso -2Baniso -3
1--8.3954 Å20 Å20 Å2
2---8.3954 Å20 Å2
3---16.7908 Å2
Refine analyzeLuzzati coordinate error obs: 0.525 Å
Refinement stepCycle: LAST / Resolution: 2.8→41.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms933 0 7 13 953
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01977HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.331334HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d331SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes140HARMONIC5
X-RAY DIFFRACTIONt_it977HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.77
X-RAY DIFFRACTIONt_other_torsion18.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion125SEMIHARMONIC5
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_contact1097SEMIHARMONIC4
LS refinement shellResolution: 2.8→3.13 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3104 59 5.39 %
Rwork0.2455 1035 -
all0.2491 1094 -
obs--98.6 %
Refinement TLS params.Method: refined / Origin x: 17.3436 Å / Origin y: -18.434 Å / Origin z: 0.8334 Å
111213212223313233
T0.331 Å2-0.3202 Å20.0446 Å2-0.1066 Å20.0062 Å2---0.3662 Å2
L0.8735 °20.1756 °2-0.9775 °2--0.0884 °2-0.9914 °2--21.0225 °2
S0.0528 Å °0.0886 Å °-0.087 Å °0.11 Å °0.105 Å °-0.0656 Å °-0.862 Å °-0.2311 Å °-0.1578 Å °
Refinement TLS groupSelection details: CHAIN A

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