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- PDB-3i08: Crystal structure of the S1-cleaved Notch1 Negative Regulatory Re... -

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Basic information

Entry
Database: PDB / ID: 3i08
TitleCrystal structure of the S1-cleaved Notch1 Negative Regulatory Region (NRR)
Components(Neurogenic locus notch homolog protein 1) x 2
KeywordsSIGNALING PROTEIN / SEA domain / Lin-12 Notch repeat / LNR / Heterodimerization Domain / HD / Activator / ANK repeat / Calcium / Cell membrane / Developmental protein / Differentiation / Disulfide bond / EGF-like domain / Glycoprotein / Membrane / Metal-binding / Notch signaling pathway / Nucleus / Phosphoprotein / Polymorphism / Receptor / Transcription / Transcription regulation / Transmembrane / furin / T-ALL / leukemia / oncogene / metalloprotease / gamma-secretase
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 / negative regulation of cell proliferation involved in heart morphogenesis / endocardium morphogenesis / distal tubule development / MAML1-RBP-Jkappa- ICN1 complex / cardiac chamber formation / cardiac atrium morphogenesis / pericardium morphogenesis / atrioventricular node development / cardiac ventricle morphogenesis / positive regulation of transcription of Notch receptor target / negative regulation of endothelial cell chemotaxis / glomerular mesangial cell development / CSL-Notch-Mastermind transcription factor complex / cellular response to tumor cell / positive regulation of smooth muscle cell differentiation / cardiac septum morphogenesis / 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 / cardiac muscle cell myoblast differentiation / negative regulation of stem cell differentiation / negative regulation of cell adhesion molecule production / T-helper 17 type immune response / tissue regeneration / positive regulation of cardiac epithelial to mesenchymal transition / cardiac epithelial to mesenchymal transition / regulation of cell adhesion involved in heart morphogenesis / heart trabecula morphogenesis / Pre-NOTCH Processing in Golgi / negative regulation of oligodendrocyte differentiation / interleukin-17-mediated signaling pathway / 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 / pulmonary valve morphogenesis / tube formation / determination of left/right symmetry / cardiac muscle tissue morphogenesis / oligodendrocyte differentiation / 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 / response to muramyl dipeptide / negative regulation of biomineral tissue development / astrocyte differentiation / positive regulation of BMP signaling pathway / endocardial cushion morphogenesis / 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 / transcription regulator activator activity / 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 / NOTCH3 Intracellular Domain Regulates Transcription / negative regulation of neuron differentiation / NFE2L2 regulating tumorigenic genes / heart looping / ventricular septum morphogenesis / Notch-HLH transcription pathway / Formation of paraxial mesoderm
Similarity search - Function
Ricin (A Subunit), domain 2 - #20 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #470 / Neurogenic locus notch homolog protein 1 / Notch, C-terminal / Domain of unknown function / : / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein ...Ricin (A Subunit), domain 2 - #20 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #470 / 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 / Ricin (A Subunit), domain 2 / : / Calcium-binding EGF domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Helix non-globular / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Special / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Few Secondary Structures / Irregular / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Neurogenic locus notch homolog protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGordon, W.R. / Blacklow, S.C.
CitationJournal: Plos One / Year: 2009
Title: Effects of S1 cleavage on the structure, surface export, and signaling activity of human Notch1 and Notch2.
Authors: Gordon, W.R. / Vardar-Ulu, D. / L'Heureux, S. / Ashworth, T. / Malecki, M.J. / Sanchez-Irizarry, C. / McArthur, D.G. / Histen, G. / Mitchell, J.L. / Aster, J.C. / Blacklow, S.C.
History
DepositionJun 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
B: Neurogenic locus notch homolog protein 1
C: Neurogenic locus notch homolog protein 1
D: Neurogenic locus notch homolog protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,23311
Polymers63,9574
Non-polymers2767
Water37821
1
A: Neurogenic locus notch homolog protein 1
B: Neurogenic locus notch homolog protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1346
Polymers31,9792
Non-polymers1564
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Neurogenic locus notch homolog protein 1
D: Neurogenic locus notch homolog protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0995
Polymers31,9792
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Neurogenic locus notch homolog protein 1
B: Neurogenic locus notch homolog protein 1
hetero molecules

C: Neurogenic locus notch homolog protein 1
D: Neurogenic locus notch homolog protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,23311
Polymers63,9574
Non-polymers2767
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455y-1,x,-z1
Buried area13660 Å2
ΔGint-113 kcal/mol
Surface area22690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.868, 65.868, 322.586
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112B - A1450 - 1529
2112A1450 - 1529

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Components

#1: Protein Neurogenic locus notch homolog protein 1 / Notch 1 / hN1 / Translocation-associated notch protein TAN-1 / Notch 1 extracellular truncation / ...Notch 1 / hN1 / Translocation-associated notch protein TAN-1 / Notch 1 extracellular truncation / Notch 1 intracellular domain


Mass: 24595.336 Da / Num. of mol.: 2 / Fragment: Notch1 NRR (Residues 1446-1665)
Source method: isolated from a genetically manipulated source
Details: Cloned into pet15b containing an N-terminal His6 tag with a TEV protease site. Upon cleavage, a non-native Glycine remains at the N-terminus. Protein was expressed, purified from inclusion ...Details: Cloned into pet15b containing an N-terminal His6 tag with a TEV protease site. Upon cleavage, a non-native Glycine remains at the N-terminus. Protein was expressed, purified from inclusion bodies, refolded and purified as previously described. Recombinant furin incubated with the Notch1 NRR overnight, and size exclusion chromatography was used to purify the complex.
Source: (gene. exp.) Homo sapiens (human) / Gene: human Notch1, NOTCH1, TAN1 / Plasmid: hN1 NRR full-length / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: P46531
#2: Protein Neurogenic locus notch homolog protein 1


Mass: 7383.235 Da / Num. of mol.: 2 / Fragment: Notch1 NRR (Residues 1666-1734)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: human Notch1, NOTCH1, TAN1 / Plasmid: hN1 NRR full-length / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: P46531
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PRECURSOR STRUCTURE WAS CLEAVED IN VITRO BY FURIN PROTEASE. FURIN CLEAVES AT R1665 PRIMARILY, ...THE PRECURSOR STRUCTURE WAS CLEAVED IN VITRO BY FURIN PROTEASE. FURIN CLEAVES AT R1665 PRIMARILY, BUT A MINOR CLEAVAGE WAS OBSERVED AT R1634 VIA MASS SPECTROMETRY OF THE CRYSTALLIZED PROTEIN.
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: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1M NaOAc, 2.0 M NaCl, 10% glycerol, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→46 Å / Num. all: 11941 / Num. obs: 11928 / % possible obs: 94.4 % / Redundancy: 5.4 % / Biso Wilson estimate: 74.9 Å2 / Rsym value: 0.132 / Net I/σ(I): 9.9
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 11320 / Rsym value: 0.518 / % possible all: 97.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0093refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Notch1 NRR deletion (3eto)

3eto


Resolution: 3.2→46.32 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.878 / Occupancy max: 1 / Occupancy min: 1 / SU B: 20.757 / SU ML: 0.364 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.535 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.286 602 5 %RANDOM
Rwork0.229 ---
obs0.232 11922 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.83 Å2 / Biso mean: 76.809 Å2 / Biso min: 38.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 3.2→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3566 0 7 21 3594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213670
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.9224995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9615462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.80925.337193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.88215545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4211515
X-RAY DIFFRACTIONr_chiral_restr0.1260.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212917
X-RAY DIFFRACTIONr_mcbond_it0.7371.52312
X-RAY DIFFRACTIONr_mcangle_it1.4423677
X-RAY DIFFRACTIONr_scbond_it1.66231358
X-RAY DIFFRACTIONr_scangle_it2.8914.51318
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
316TIGHT POSITIONAL0.030.05
277MEDIUM POSITIONAL0.040.5
316TIGHT THERMAL0.060.5
277MEDIUM THERMAL0.072
LS refinement shellResolution: 3.203→3.286 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 35 -
Rwork0.281 833 -
all-868 -
obs--96.55 %

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