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- PDB-2rqz: Structure of sugar modified epidermal growth factor-like repeat 1... -

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Basic information

Entry
Database: PDB / ID: 2rqz
TitleStructure of sugar modified epidermal growth factor-like repeat 12 of mouse Notch-1 receptor
ComponentsNeurogenic locus notch homolog protein 1
KeywordsRECEPTOR / NOTCH / GLYCOPEPTIDE / O-LINKED FUCOSE / ACTIVATOR / FRINGE / ANK REPEAT / DEVELOPMENTAL PROTEIN / DIFFERENTIATION / EGF-LIKE DOMAIN / GLYCOPROTEIN / METAL-BINDING / NOTCH SIGNALING PATHWAY / NUCLEUS / PHOSPHORYLATION / TRANSCRIPTION / TRANSCRIPTION REGULATION / TRANSMEMBRANE / Cell membrane / Disulfide bond / Phosphoprotein
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 / venous endothelial cell differentiation / retinal cone cell differentiation / arterial endothelial cell differentiation / 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 / 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 / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / 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 / collecting duct development / negative regulation of extracellular matrix constituent secretion / cellular response to tumor cell / Notch-HLH transcription pathway / positive regulation of apoptotic process involved in morphogenesis / compartment pattern specification / vasculogenesis involved in coronary vascular morphogenesis / T-helper 17 type immune response / endocardial cushion development / regulation of extracellular matrix assembly / chemical synaptic transmission, postsynaptic / 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 / epidermal cell fate specification / mesenchymal cell development / negative regulation of collagen biosynthetic process / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / regulation of Notch signaling pathway / negative regulation of myotube differentiation / left/right axis specification / somatic stem cell division / negative regulation of cell adhesion molecule production / negative regulation of cardiac muscle hypertrophy / interleukin-17-mediated signaling pathway / positive regulation of endothelial cell differentiation / apoptotic process involved in embryonic digit morphogenesis / endocardium development / positive regulation of cardiac epithelial to mesenchymal transition / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / cardiac epithelial to mesenchymal transition / glial cell differentiation / neuron fate commitment / negative regulation of catalytic activity / pericardium morphogenesis / cardiac atrium morphogenesis / cardiac muscle cell myoblast differentiation / negative regulation of calcium ion-dependent exocytosis / cellular response to follicle-stimulating hormone stimulus / neuronal stem cell population maintenance / tissue regeneration / calcium-ion regulated exocytosis / pulmonary valve morphogenesis / negative regulation of oligodendrocyte differentiation / positive regulation of astrocyte differentiation / negative regulation of biomineral tissue development / regulation of stem cell proliferation / heart trabecula morphogenesis / coronary artery morphogenesis / luteolysis / negative regulation of cell-cell adhesion mediated by cadherin / endoderm development / prostate gland epithelium morphogenesis / cardiac muscle tissue 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 ...: / 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 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)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsShimizu, K. / Fujitani, N. / Hosoguchi, K. / Nishimura, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Chemical Synthesis, Folding, and Structural Insights into O-Fucosylated Epidermal Growth Factor-like Repeat 12 of Mouse Notch-1 Receptor
Authors: Hiruma-Shimizu, K. / Hosoguchi, K. / Liu, Y. / Fujitani, N. / Ohta, T. / Hinou, H. / Matsushita, T. / Shimizu, H. / Feizi, T. / Nishimura, S.
History
DepositionFeb 26, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_conn
Item: _chem_comp.type / _pdbx_database_status.status_code_cs ..._chem_comp.type / _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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)4,5862
Polymers4,2191
Non-polymers3671
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 4218.697 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN EGF-LIKE repeat 12 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q01705
#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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1422D 1H-1H TOCSY
NMR detailsText: The structure was determined using a combination NOE and D2O exchange experiment.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.55mM NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1; 0.55mM SUGAR (2-MER); 90% H2O/10% D2O90% H2O/10% D2O
20.55mM NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1; 0.55mM SUGAR (2-MER); 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.55 mMNEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1-11
0.55 mMSUGAR (2-MER)-21
0.55 mMNEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1-32
0.55 mMSUGAR (2-MER)-42
Sample conditionsIonic strength: 0 / pH: 5.3 / Pressure: AMBIENT / Temperature: 300 K

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NMR measurement

NMR spectrometerType: BRUKER AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1 / Details: Both sugar rings were fixed in chair conformation.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20 / Representative conformer: 1

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