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- PDB-7abv: Structure of the S1-cleaved mouse Notch1 Negative Regulatory Regi... -

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Basic information

Entry
Database: PDB / ID: 7abv
TitleStructure of the S1-cleaved mouse Notch1 Negative Regulatory Region (NRR)
ComponentsNeurogenic locus notch homolog protein 1
KeywordsSIGNALING PROTEIN / Type I transmembrane protein / Developmental protein / Calcium binding
Function / homology
Function and homology information


Pre-NOTCH Processing in Golgi / regulation of cardioblast proliferation / regulation of inner ear auditory receptor cell differentiation / positive regulation of ephrin receptor signaling pathway / positive regulation of glial cell differentiation / osteoblast fate commitment / venous blood vessel morphogenesis / Activated NOTCH1 Transmits Signal to the Nucleus / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis ...Pre-NOTCH Processing in Golgi / regulation of cardioblast proliferation / regulation of inner ear auditory receptor cell differentiation / positive regulation of ephrin receptor signaling pathway / positive regulation of glial cell differentiation / osteoblast fate commitment / venous blood vessel morphogenesis / Activated NOTCH1 Transmits Signal to the Nucleus / 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 / 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 / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / 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 / Notch-HLH transcription pathway / compartment pattern specification / vasculogenesis involved in coronary vascular morphogenesis / T-helper 17 type immune response / endocardial cushion development / regulation of extracellular matrix assembly / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / cardiac ventricle morphogenesis / positive regulation of smooth muscle cell differentiation / cardiac left ventricle morphogenesis / mesenchymal cell development / regulation of Notch signaling pathway / 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 / apoptotic process involved in embryonic digit morphogenesis / endocardium development / glial cell differentiation / positive regulation of cardiac epithelial to mesenchymal transition / cardiac epithelial to mesenchymal transition / cellular response to follicle-stimulating hormone stimulus / negative regulation of calcium ion-dependent exocytosis / neuron fate commitment / pericardium morphogenesis / cardiac atrium morphogenesis / cardiac muscle cell myoblast differentiation / 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
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 / 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 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
Similarity search - Domain/homology
Neurogenic locus notch homolog protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.065 Å
AuthorsZeronian, M.R. / Janssen, B.J.C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Notch-Jagged signaling complex defined by an interaction mosaic.
Authors: Zeronian, M.R. / Klykov, O. / Portell I de Montserrat, J. / Konijnenberg, M.J. / Gaur, A. / Scheltema, R.A. / Janssen, B.J.C.
History
DepositionSep 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: 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.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)32,0616
Polymers31,4981
Non-polymers5635
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint6 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.724, 65.724, 161.683
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-3176-

HOH

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Components

#1: Protein Neurogenic locus notch homolog protein 1 / Notch 1 / Motch A / mT14 / p300


Mass: 31497.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Notch1, Motch / Production host: Homo sapiens (human) / References: UniProt: Q01705
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.77 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2.0 M sodium chloride, 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.06998 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06998 Å / Relative weight: 1
ReflectionResolution: 2.065→60.886 Å / Num. obs: 15144 / % possible obs: 91.5 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.03 / Rrim(I) all: 0.109 / Net I/σ(I): 14.6
Reflection shellResolution: 2.065→2.296 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1.431 / Num. unique obs: 757 / CC1/2: 0.77 / Rpim(I) all: 0.43 / Rrim(I) all: 1.496 / % possible all: 64.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
MOLREPphasing
STARANISOdata scaling
Aimlessdata scaling
XDSdata reduction
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ETO

3eto


Resolution: 2.065→60.885 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.208
RfactorNum. reflection% reflection
Rfree0.2375 795 5.25 %
Rwork0.196 14348 -
all0.198 --
obs-15143 66.922 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 57.792 Å2
Baniso -1Baniso -2Baniso -3
1--0.597 Å20 Å20 Å2
2---0.597 Å2-0 Å2
3---1.194 Å2
Refinement stepCycle: LAST / Resolution: 2.065→60.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 31 77 1904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121877
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.6432557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3895230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7424.857105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26815283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.636156
X-RAY DIFFRACTIONr_chiral_restr0.1040.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021483
X-RAY DIFFRACTIONr_nbd_refined0.2350.2889
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21305
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2106
X-RAY DIFFRACTIONr_metal_ion_refined0.1290.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.20.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1490.27
X-RAY DIFFRACTIONr_mcbond_it1.6233.144926
X-RAY DIFFRACTIONr_mcangle_it2.724.7061154
X-RAY DIFFRACTIONr_scbond_it2.1963.424948
X-RAY DIFFRACTIONr_scangle_it3.4615.0581400
X-RAY DIFFRACTIONr_lrange_it6.21844.1482880
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.065-2.1190.19940.306940.30116440.8330.8275.96110.3
2.119-2.1770.363150.2811740.28815750.8670.862120.276
2.177-2.240.31120.2842430.28515410.8660.85316.54770.276
2.24-2.3080.278180.2552880.25715010.8490.88820.38640.246
2.308-2.3840.251370.2645870.26314610.8680.87942.71050.246
2.384-2.4680.306410.2537600.25614200.8430.89456.40850.225
2.468-2.5610.279570.2610950.26113800.8730.8883.47830.236
2.561-2.6650.3590.24712610.2513330.8840.88799.02480.223
2.665-2.7830.287650.2411970.24212620.9030.8971000.209
2.783-2.9190.265670.21111590.21412260.9150.9241000.186
2.919-3.0760.234670.20110960.20311640.9140.93599.91410.178
3.076-3.2620.25630.21210440.21411070.9130.9361000.193
3.262-3.4870.226500.1949970.19510470.9340.9531000.178
3.487-3.7650.191450.1877680.1879820.9480.96282.79020.175
3.765-4.1230.19340.1566870.1589130.9590.9778.97040.153
4.123-4.6070.213530.1617740.1648270.9560.9661000.161
4.607-5.3140.248290.1757160.1787450.9460.9591000.181
5.314-6.4970.238370.1926060.1956430.9290.9531000.199
6.497-9.1360.262260.1734940.1775210.9460.9699.80810.193
9.136-60.8850.225160.2013070.2033290.9510.95998.17630.238
Refinement TLS params.Method: refined / Origin x: 1.9 Å / Origin y: 17.619 Å / Origin z: -21.405 Å
111213212223313233
T0.3832 Å2-0.0061 Å20.0541 Å2-0.0562 Å2-0.0428 Å2--0.0636 Å2
L2.7443 °20.9533 °2-1.3979 °2-2.6715 °2-1.3213 °2--2.3221 °2
S-0.1845 Å °0.239 Å °-0.3285 Å °-0.7653 Å °0.1718 Å °-0.1435 Å °0.3315 Å °-0.0202 Å °0.0127 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA1448 - 1717
2X-RAY DIFFRACTION1ALLAaA3001
3X-RAY DIFFRACTION1ALLAbA3002
4X-RAY DIFFRACTION1ALLAcA3003
5X-RAY DIFFRACTION1ALLAdA3004

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