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- PDB-7alj: Structure of Drosophila Notch EGF domains 11-13 -

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Basic information

Entry
Database: PDB / ID: 7alj
TitleStructure of Drosophila Notch EGF domains 11-13
ComponentsNeurogenic locus Notch protein
KeywordsSIGNALING PROTEIN / Notch Notch LIgand EGF domains
Function / homology
Function and homology information


response to symbiont / neuroblast fate specification / epithelial cell type specification, open tracheal system / lamellocyte differentiation / regulation of cardioblast cell fate specification / positive regulation of crystal cell differentiation / negative regulation of compound eye photoreceptor development / R1/R6 cell differentiation / formation of a compartment boundary / compartment boundary maintenance ...response to symbiont / neuroblast fate specification / epithelial cell type specification, open tracheal system / lamellocyte differentiation / regulation of cardioblast cell fate specification / positive regulation of crystal cell differentiation / negative regulation of compound eye photoreceptor development / R1/R6 cell differentiation / formation of a compartment boundary / compartment boundary maintenance / follicle cell of egg chamber migration / muscle cell fate determination / imaginal disc-derived leg joint morphogenesis / eye-antennal disc development / crystal cell differentiation / R7 cell differentiation / R3/R4 cell differentiation / oocyte localization involved in germarium-derived egg chamber formation / hemocyte proliferation / negative regulation of lamellocyte differentiation / myoblast development / imaginal disc-derived male genitalia morphogenesis / germarium-derived egg chamber formation / leg disc morphogenesis / epithelial cell proliferation involved in Malpighian tubule morphogenesis / CSL-Notch-Mastermind transcription factor complex / lateral inhibition / Malpighian tubule tip cell differentiation / eye-antennal disc morphogenesis / second mitotic wave involved in compound eye morphogenesis / imaginal disc-derived wing margin morphogenesis / imaginal disc-derived leg segmentation / sensory organ precursor cell fate determination / female germ-line stem cell population maintenance / ommatidial rotation / wing disc dorsal/ventral pattern formation / wing disc pattern formation / germ-line stem-cell niche homeostasis / defense response to insect / follicle cell of egg chamber stalk formation / compound eye retinal cell programmed cell death / imaginal disc-derived leg morphogenesis / dorsal closure / chaeta morphogenesis / compound eye morphogenesis / neuroblast development / follicle cell of egg chamber development / lymph gland development / larval lymph gland hemopoiesis / neuroblast fate determination / imaginal disc-derived wing vein specification / cell dedifferentiation / dorsal appendage formation / border follicle cell migration / compound eye development / foregut morphogenesis / asymmetric cell division / chaeta development / regulation of stem cell division / imaginal disc-derived wing morphogenesis / glial cell fate determination / intestinal stem cell homeostasis / neuron fate specification / regulation of neuroblast proliferation / glial cell migration / retinal cell programmed cell death / neuron fate determination / sensory organ development / germ-line stem cell population maintenance / dorsal/ventral axis specification / glial cell differentiation / neuronal stem cell population maintenance / regulation of filopodium assembly / peripheral nervous system development / negative regulation of cell-cell adhesion mediated by cadherin / motor neuron axon guidance / regulation of growth / nervous system process / embryonic hemopoiesis / regulation of glycolytic process / muscle cell cellular homeostasis / WW domain binding / oogenesis / morphogenesis of an epithelial fold / positive regulation of neuroblast proliferation / histone acetyltransferase binding / mesoderm development / regulation of cell differentiation / regulation of neurogenesis / endocytic vesicle / neuroblast proliferation / cell fate commitment / long-term memory / positive regulation of G1/S transition of mitotic cell cycle / Notch signaling pathway / multivesicular body / axon guidance / regulation of mitotic cell cycle / actin filament organization / determination of adult lifespan
Similarity search - Function
: / Notch, C-terminal / Domain of unknown function / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein / NOD / NODP ...: / 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 protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsSuckling, R. / Johnson, S. / Lea, S.M.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/L001187/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR-R009317/1 United Kingdom
Wellcome Trust100298 United Kingdom
CitationJournal: Embo Rep. / Year: 2021
Title: The conserved C2 phospholipid-binding domain in Delta contributes to robust Notch signalling.
Authors: Martins, T. / Meng, Y. / Korona, B. / Suckling, R. / Johnson, S. / Handford, P.A. / Lea, S.M. / Bray, S.J.
History
DepositionOct 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc / pdbx_entity_branch_descriptor
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6768
Polymers12,4971
Non-polymers1,1797
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint1 kcal/mol
Surface area8130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.820, 31.286, 21.795
Angle α, β, γ (deg.)90.000, 90.769, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neurogenic locus Notch protein / Notch


Mass: 12496.749 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: N, CG3936 / Cell line (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P07207

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Sugars , 4 types, 5 molecules

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


Type: oligosaccharide / Mass: 312.271 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DXylpb1-3DGlcpb1-Glycam 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
[]{[(3+1)][b-D-Glcp]{[(3+1)][a-D-Xylp]{}}}LINUCSPDB-CARE
#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.: 1 / 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
#5: 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
#6: 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

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Non-polymers , 2 types, 99 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M MES 6.5, 1.8M Ammonium sulphate, 0.01M Cobalt chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→45.2 Å / Num. obs: 18808 / % possible obs: 98.38 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.54 Å2 / CC1/2: 0.996 / Net I/σ(I): 7.75
Reflection shellResolution: 1.523→1.577 Å / Mean I/σ(I) obs: 1.68 / Num. unique obs: 1771 / CC1/2: 0.701

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Processing

Software
NameVersionClassification
PHENIXdev_3965refinement
PHENIXdev_3965refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vj3

2vj3


Resolution: 1.52→45.2 Å / SU ML: 0.239 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.9919
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2414 962 5.16 %
Rwork0.2014 17692 -
obs0.2034 18654 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.83 Å2
Refinement stepCycle: LAST / Resolution: 1.52→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms845 0 71 97 1013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172942
X-RAY DIFFRACTIONf_angle_d1.44631278
X-RAY DIFFRACTIONf_chiral_restr0.0869146
X-RAY DIFFRACTIONf_plane_restr0.0107172
X-RAY DIFFRACTIONf_dihedral_angle_d6.5598145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.60.4011310.36182373X-RAY DIFFRACTION94.03
1.6-1.70.29611400.27632524X-RAY DIFFRACTION98.89
1.7-1.840.27741360.23282534X-RAY DIFFRACTION98.52
1.84-2.020.2611370.21742519X-RAY DIFFRACTION99.33
2.02-2.310.24741290.19362554X-RAY DIFFRACTION99.85
2.31-2.910.25651410.20352575X-RAY DIFFRACTION99.41
2.91-45.20.2051480.17522613X-RAY DIFFRACTION98.68

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