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- PDB-9b3n: Human Notch-1 EGFs 20-24 -

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Basic information

Entry
Database: PDB / ID: 9b3n
TitleHuman Notch-1 EGFs 20-24
ComponentsNeurogenic locus notch homolog protein 1
KeywordsSIGNALING PROTEIN / Notch / EGF / Calcium-binding
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 / endocardium development / apoptotic process involved in embryonic digit morphogenesis / 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 / cellular response to follicle-stimulating hormone stimulus / negative regulation of calcium ion-dependent exocytosis / cardiac muscle cell myoblast differentiation / 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 / : / Calcium-binding EGF 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
Similarity search - Domain/homology
beta-D-glucopyranose / alpha-L-fucopyranose / Neurogenic locus notch homolog protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsJohnson, S. / Suckling, R. / Handford, P.A. / Lea, S.M.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/R009317/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/V008935/1 United Kingdom
Wellcome Trust100298 United Kingdom
CitationJournal: Structure / Year: 2024
Title: Structural and functional studies of the EGF20-27 region reveal new features of the human Notch receptor important for optimal activation.
Authors: Bo, Z. / Rowntree, T. / Johnson, S. / Nurmahdi, H. / Suckling, R.J. / Hill, J. / Korona, B. / Weisshuhn, P.C. / Sheppard, D. / Meng, Y. / Liang, S. / Lowe, E.D. / Lea, S.M. / Redfield, C. / Handford, P.A.
History
DepositionMar 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 18, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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)22,84513
Polymers21,4121
Non-polymers1,43312
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.030, 35.080, 63.890
Angle α, β, γ (deg.)99.710, 92.350, 96.860
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 21411.588 Da / Num. of mol.: 1 / Fragment: Human Notch1 EGFs 20-24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOTCH1, TAN1 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P46531

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Sugars , 3 types, 6 molecules

#2: Polysaccharide beta-D-xylopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 312.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a212h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(3+1)][b-D-Xylp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar
ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 294 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Imidazole Malate pH 6 8% (w/v) PEG4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.5→62.9 Å / Num. obs: 36167 / % possible obs: 95.2 % / Redundancy: 2.6 % / Biso Wilson estimate: 21.09 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.056 / Net I/σ(I): 7.7
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2764 / CC1/2: 0.884

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→62.85 Å / SU ML: 0.1421 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.5967
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1979 1828 5.05 %
Rwork0.1755 34339 -
obs0.1767 36167 94.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.62 Å2
Refinement stepCycle: LAST / Resolution: 1.5→62.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1420 0 83 288 1791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01351547
X-RAY DIFFRACTIONf_angle_d1.46442102
X-RAY DIFFRACTIONf_chiral_restr0.081236
X-RAY DIFFRACTIONf_plane_restr0.0134283
X-RAY DIFFRACTIONf_dihedral_angle_d20.7668661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.31931490.29522615X-RAY DIFFRACTION94.11
1.54-1.590.28821340.27152596X-RAY DIFFRACTION93.49
1.59-1.640.28851520.23182642X-RAY DIFFRACTION94.33
1.64-1.70.2511370.20632607X-RAY DIFFRACTION94.78
1.7-1.760.24071310.20552695X-RAY DIFFRACTION94.67
1.76-1.840.22251200.19342644X-RAY DIFFRACTION95.57
1.84-1.940.26251460.18542634X-RAY DIFFRACTION95.08
1.94-2.060.21451310.18382696X-RAY DIFFRACTION95.7
2.06-2.220.23791470.17292621X-RAY DIFFRACTION95.32
2.22-2.450.17111500.17592611X-RAY DIFFRACTION94.75
2.45-2.80.2151480.17842680X-RAY DIFFRACTION95.51
2.8-3.530.19161450.16962642X-RAY DIFFRACTION95.22
3.53-62.850.1521380.15222656X-RAY DIFFRACTION95.82
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.47489772368-1.0756579078-1.070691255915.70819258796-4.36125201994.849189142350.05449058103380.0913786692087-0.10186352675-0.4663104806540.11733472920.1102670433180.373144655301-0.105084710088-0.1141919588880.381913935011-0.0414900571181-0.03917049655550.1712100650930.007054045315040.15890694827-16.0230897849-56.2864856954-54.6105908069
24.714013856185.439475504976.868228764716.106596716536.707307064718.583569177310.420447565069-0.227918196187-0.08035163748610.342218494412-0.2567191006430.0515833355490.737864319584-0.246147314382-0.181660053730.273549952179-0.043506498993-0.01167895126170.248903998313-0.03006842802590.204034767758-6.78414401786-41.174196815-36.544883898
37.305641774691.243600153844.169042786430.8088737273691.899646475447.566675171590.0918005703418-0.3059738463480.4025501854530.356841438401-0.2323048542890.139987699022-0.1680626743350.1077928616280.1644320648620.230456756166-0.05446052847630.01872739180150.2130954467760.008922536703990.1500403102966.47554817838-26.5963580736-23.4446670146
48.278303288738.528377602027.345920070878.560212744927.404861010356.385654619430.503380506128-0.2827560542120.2495505330840.474095232509-0.3430068281760.2040550564550.293320888916-0.102323261195-0.1174807418310.482870669359-0.1232503843830.06005641800470.310133470566-0.03233228798870.32923610719313.4004150708-11.5915188053-17.7816178428
50.3236295559361.298929693521.189222536064.911934094196.302925053747.67117282001-0.06732885799450.102815176949-0.0647331349641-0.266199831480.207094674362-0.134359634397-0.4487272455490.125684671251-0.1336835275110.33188695253-0.0311681988802-0.0286334442460.2106950562590.006952995720460.18056055461226.38342990478.99457216214-3.36378668156
63.987815905550.445442358452-1.276267990316.687072385743.80760714162.801015886350.0646841469664-0.2989980035980.0976814230425-0.02234983683330.180671586935-0.232402797381-0.2474067769540.34595074901-0.2667828015510.166964458902-0.007087457028990.02292940227110.1631080299620.01434478849520.15878234358928.81067405428.169881039224.3854396454
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 755 through 778 )755 - 7781 - 24
22chain 'A' and (resid 779 through 816 )779 - 81625 - 62
33chain 'A' and (resid 817 through 836 )817 - 83663 - 82
44chain 'A' and (resid 837 through 861 )837 - 86183 - 107
55chain 'A' and (resid 862 through 914 )862 - 914108 - 160
66chain 'A' and (resid 915 through 949 )915 - 949161 - 195

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