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- PDB-7alk: Structure of Drosophila C2-DSL-EGF1 -

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Basic information

Entry
Database: PDB / ID: 7alk
TitleStructure of Drosophila C2-DSL-EGF1
ComponentsNeurogenic locus protein delta
KeywordsSIGNALING PROTEIN / Delta Notch Ligand C2 / DSL and EGF domains
Function / homology
Function and homology information


compound eye photoreceptor development / R7 cell differentiation / R3/R4 cell differentiation / apposition of dorsal and ventral imaginal disc-derived wing surfaces / oocyte localization involved in germarium-derived egg chamber formation / compound eye retinal cell programmed cell death / regulation of establishment of planar polarity / lateral inhibition / second mitotic wave involved in compound eye morphogenesis / imaginal disc-derived wing margin morphogenesis ...compound eye photoreceptor development / R7 cell differentiation / R3/R4 cell differentiation / apposition of dorsal and ventral imaginal disc-derived wing surfaces / oocyte localization involved in germarium-derived egg chamber formation / compound eye retinal cell programmed cell death / regulation of establishment of planar polarity / lateral inhibition / second mitotic wave involved in compound eye morphogenesis / imaginal disc-derived wing margin morphogenesis / imaginal disc-derived leg segmentation / wing disc dorsal/ventral pattern formation / antennal morphogenesis / follicle cell of egg chamber stalk formation / imaginal disc-derived leg morphogenesis / chaeta morphogenesis / follicle cell of egg chamber development / wing disc anterior/posterior pattern formation / sensory organ development / neuroblast fate determination / border follicle cell migration / asymmetric cell division / imaginal disc-derived wing morphogenesis / glycosphingolipid binding / neuron fate specification / glial cell migration / germ-line stem cell population maintenance / apical cortex / peripheral nervous system development / Notch binding / cell fate specification / oogenesis / mesoderm development / endocytic vesicle / Notch signaling pathway / positive regulation of mitotic cell cycle / actin filament organization / stem cell differentiation / cytoplasmic vesicle / early endosome / endosome / receptor ligand activity / positive regulation of cell population proliferation / calcium ion binding / cell surface / membrane / plasma membrane
Similarity search - Function
Delta/Serrate/lag-2 (DSL) protein / Notch ligand, N-terminal domain / Delta serrate ligand / N terminus of Notch ligand C2-like domain / DSL domain profile. / delta serrate ligand / Delta-like/Jagged, EGF-like domain / : / EGF-like, conserved site / Human growth factor-like EGF ...Delta/Serrate/lag-2 (DSL) protein / Notch ligand, N-terminal domain / Delta serrate ligand / N terminus of Notch ligand C2-like domain / DSL domain profile. / delta serrate ligand / Delta-like/Jagged, EGF-like domain / : / EGF-like, conserved site / Human growth factor-like EGF / 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. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain
Similarity search - Domain/homology
Neurogenic locus protein delta
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 / diffrn_source / pdbx_database_proc
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 / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurogenic locus protein delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9194
Polymers26,4191
Non-polymers1,4993
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint23 kcal/mol
Surface area14640 Å2
Unit cell
Length a, b, c (Å)30.990, 86.736, 47.558
Angle α, β, γ (deg.)90.000, 94.271, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Neurogenic locus protein delta / Delta


Mass: 26419.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dl, CG3619 / Cell line (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P10041
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#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.: 2 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris pH 8.5, 0.2M MgCl2, 30% PEG4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→29.11 Å / Num. obs: 5066 / % possible obs: 99.84 % / Redundancy: 3.4 % / Biso Wilson estimate: 33.66 Å2 / CC1/2: 0.952 / Net I/σ(I): 4.55
Reflection shellResolution: 3→3.107 Å / Mean I/σ(I) obs: 0.85 / Num. unique obs: 520 / CC1/2: 0.483

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Processing

Software
NameVersionClassification
PHENIXdev_3965refinement
PHENIXdev_3965refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MVX

5mvx


Resolution: 3→29.11 Å / SU ML: 0.5048 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.9094
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2968 287 5.67 %
Rwork0.2407 4779 -
obs0.2437 5066 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.61 Å2
Refinement stepCycle: LAST / Resolution: 3→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1801 0 99 2 1902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031941
X-RAY DIFFRACTIONf_angle_d0.58292624
X-RAY DIFFRACTIONf_chiral_restr0.0526302
X-RAY DIFFRACTIONf_plane_restr0.0031330
X-RAY DIFFRACTIONf_dihedral_angle_d14.9412310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.780.33581520.27842361X-RAY DIFFRACTION99.88
3.78-29.110.26961350.2162418X-RAY DIFFRACTION100

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