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- PDB-4d0e: Human Notch1 EGF domains 11-13 mutant GlcNAc-fucose disaccharide ... -

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Entry
Database: PDB / ID: 4d0e
TitleHuman Notch1 EGF domains 11-13 mutant GlcNAc-fucose disaccharide modified at T466
ComponentsNEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1
KeywordsTRANSCRIPTION / METAL-BINDING / TRANSMEMBRANE / DEVELOPMENTAL / 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 / 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 / pericardium morphogenesis / negative regulation of endothelial cell chemotaxis / atrioventricular node development / cardiac ventricle morphogenesis / positive regulation of transcription of Notch receptor target / cardiac septum morphogenesis / glomerular mesangial cell development / cellular response to tumor cell / positive regulation of smooth muscle cell differentiation / vasculogenesis involved in coronary vascular morphogenesis / negative regulation of extracellular matrix constituent secretion / regulation of extracellular matrix assembly / chemical synaptic transmission, postsynaptic / positive regulation of apoptotic process involved in morphogenesis / endocardial cell differentiation / left/right axis specification / epithelial to mesenchymal transition involved in endocardial cushion formation / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / positive regulation of endothelial cell differentiation / cardiac left ventricle morphogenesis / negative regulation of myotube differentiation / coronary vein morphogenesis / negative regulation of glial cell proliferation / cardiac vascular smooth muscle cell development / neuronal stem cell population maintenance / endocardium development / positive regulation of astrocyte differentiation / negative regulation of cell adhesion molecule production / negative regulation of stem cell differentiation / cardiac muscle cell myoblast differentiation / tissue regeneration / T-helper 17 type immune response / positive regulation of cardiac epithelial to mesenchymal transition / cardiac epithelial to mesenchymal transition / heart trabecula morphogenesis / negative regulation of oligodendrocyte differentiation / 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 / cellular response to follicle-stimulating hormone stimulus / negative regulation of collagen biosynthetic process / negative regulation of cardiac muscle hypertrophy / luteolysis / determination of left/right symmetry / pulmonary valve morphogenesis / tube formation / oligodendrocyte differentiation / cardiac muscle tissue morphogenesis / atrioventricular valve morphogenesis / ventricular trabecula myocardium morphogenesis / coronary artery morphogenesis / negative regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion mediated by cadherin / negative regulation of ossification / negative regulation of biomineral tissue development / positive regulation of BMP signaling pathway / response to muramyl dipeptide / astrocyte differentiation / endocardial cushion morphogenesis / transcription regulator activator activity / homeostasis of number of cells within a tissue / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / Notch binding / Regulation of NFE2L2 gene expression / NOTCH4 Intracellular Domain Regulates Transcription / aortic valve morphogenesis / positive regulation of neuroblast proliferation / negative regulation of cold-induced thermogenesis / negative regulation of neuron differentiation / NOTCH3 Intracellular Domain Regulates Transcription / NFE2L2 regulating tumorigenic genes / heart looping / ventricular septum morphogenesis / Notch-HLH transcription pathway / 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 / : / Calcium-binding EGF domain / Laminin / Laminin / 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. / Ribbon / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / 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: 1.61 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 1.1Jun 4, 2014Group: Database references
Revision 1.2Feb 7, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,3856
Polymers14,8581
Non-polymers5285
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.440, 28.440, 282.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1535-

CA

21A-2112-

HOH

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Components

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


Mass: 14857.604 Da / Num. of mol.: 1 / Fragment: EGF 11-13, RESIDUES 411-526
Source method: isolated from a genetically manipulated source
Details: GLCNAC, O-FUCOSE DISSACCHARIDE AT T466 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P46531
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-3LFucpa1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1221m-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-L-Fucp]{[(3+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.82 % / Description: NONE
Crystal growpH: 6 / Details: pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.61→47.07 Å / Num. obs: 16974 / % possible obs: 96.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.3
Reflection shellResolution: 1.61→1.65 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.3 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VJ3

2vj3


Resolution: 1.61→47.07 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.912 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27031 889 5 %RANDOM
Rwork0.23052 ---
obs0.23238 16974 95.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.61→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms914 0 28 141 1083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02966
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1031.9741319
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6255121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.48626.66748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3815146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.665152
X-RAY DIFFRACTIONr_chiral_restr0.0710.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021739
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.61→1.652 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 54 -
Rwork0.42 1031 -
obs--92.89 %

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