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- PDB-3eto: 2 Angstrom Xray structure of the NOTCH1 Negative Regulatory Regio... -

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Basic information

Entry
Database: PDB / ID: 3eto
Title2 Angstrom Xray structure of the NOTCH1 Negative Regulatory Region (NRR)
ComponentsNeurogenic locus notch homolog protein 1
KeywordsSIGNALING PROTEIN / alpha-beta sandwich / HD domain / LNR repeat / calcium-binding / SEA domain / autoinhibition / Activator / T-ALL / leukemia / oncogene / ANK repeat / Developmental protein / Differentiation / EGF-like domain / Glycoprotein / Membrane / Metal-binding / Notch signaling pathway / Nucleus / Phosphoprotein / Receptor / Transcription / Transcription regulation / Transmembrane
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
GMP Synthetase; Chain A, domain 3 - #320 / Alpha-Beta Plaits - #3310 / Neurogenic locus notch homolog protein 1 / Notch, C-terminal / Domain of unknown function / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein ...GMP Synthetase; Chain A, domain 3 - #320 / Alpha-Beta Plaits - #3310 / 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) / GMP Synthetase; Chain A, domain 3 / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha 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 Å
AuthorsGordon, W.R. / Blacklow, S.C.
CitationJournal: Blood / Year: 2009
Title: Structure of the Notch1-negative regulatory region: implications for normal activation and pathogenic signaling in T-ALL.
Authors: Gordon, W.R. / Roy, M. / Vardar-Ulu, D. / Garfinkel, M. / Mansour, M.R. / Aster, J.C. / Blacklow, S.C.
History
DepositionOct 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurogenic locus notch homolog protein 1
B: Neurogenic locus notch homolog protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,54117
Polymers53,5852
Non-polymers95615
Water4,882271
1
A: Neurogenic locus notch homolog protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3179
Polymers26,7931
Non-polymers5248
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neurogenic locus notch homolog protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2258
Polymers26,7931
Non-polymers4327
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)169.927, 91.759, 59.844
Angle α, β, γ (deg.)90.00, 109.38, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: GLU / End label comp-ID: GLU

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARG4AA1569 - 1720124 - 228
21ARGARG4BB1569 - 1720124 - 228
12ASNASN5AA1470 - 156825 - 123
22ASNASN5BB1470 - 156825 - 123

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Components

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


Mass: 26792.709 Da / Num. of mol.: 2
Fragment: NOTCH1 Negative Regulatory Region, residues 1447-1734
Source method: isolated from a genetically manipulated source
Details: This construct contains an N-terminal His6 tag, followed by a TEV protease cleavage site. TEV cleavage results in a non-native Gly at the N-terminus. The construct encodes Glu1447 to Gln1734 ...Details: This construct contains an N-terminal His6 tag, followed by a TEV protease cleavage site. TEV cleavage results in a non-native Gly at the N-terminus. The construct encodes Glu1447 to Gln1734 and has been engineered to remove the unstructured loop containing the furin cleavage site; residues 1623-1669 removed.
Source: (gene. exp.) Homo sapiens (human) / Gene: NOTCH1, TAN1 / Plasmid: Novagen pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta pLysS / References: UniProt: P46531
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT CONTAINS AN N-TERMINAL HIS6 TAG, FOLLOWED BY A TEV PROTEASE CLEAVAGE SITE. TEV ...THIS CONSTRUCT CONTAINS AN N-TERMINAL HIS6 TAG, FOLLOWED BY A TEV PROTEASE CLEAVAGE SITE. TEV CLEAVAGE RESULTS IN A NON-NATIVE GLY AT THE N-TERMINUS. THE CONSTRUCT ENCODES GLU1447 TO GLN1734 AND HAS BEEN ENGINEERED TO REMOVE THE UNSTRUCTURED LOOP CONTAINING THE FURIN CLEAVAGE SITE. RESIDUES 1623-1669 WERE REMOVED.

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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: 4.11 Å3/Da / Density % sol: 70.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1M Sodium acetate pH 4.0, 1.0-1.5M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 54862 / % possible obs: 93.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 33.7 Å2 / Rsym value: 0.046 / Net I/σ(I): 23.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.202 / % possible all: 60.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.4.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OO4

2oo4


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.336 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25185 2761 5 %RANDOM
Rwork0.21108 ---
obs0.21313 52098 93.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.644 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å20 Å2-0.49 Å2
2--0.4 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3563 0 50 271 3884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213700
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.934974
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0575460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78325.258194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.615553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.281516
X-RAY DIFFRACTIONr_chiral_restr0.1030.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212898
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_it0.9831.52300
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.80323654
X-RAY DIFFRACTIONr_scbond_it2.57631400
X-RAY DIFFRACTIONr_scangle_it3.9324.51320
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1219medium positional0.220.5
A373loose positional0.375
B1219medium thermal1.862
B373loose thermal2.0710
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 118 -
Rwork0.249 2340 -
obs--57.56 %

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