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- PDB-7alt: Structure of Drosophila Serrate C2-DSL-EGF1-EGF2 -

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Basic information

Entry
Database: PDB / ID: 7alt
TitleStructure of Drosophila Serrate C2-DSL-EGF1-EGF2
ComponentsProtein serrate
KeywordsSIGNALING PROTEIN / Serrate Notch Ligand C2 / DSL and EGF domains
Function / homology
Function and homology information


larval salivary gland morphogenesis / Pre-NOTCH Processing in Golgi / NOTCH4 Activation and Transmission of Signal to the Nucleus / Negative regulation of NOTCH4 signaling / eye-antennal disc development / crystal cell differentiation / negative regulation of lamellocyte differentiation / cuticle pattern formation / lateral inhibition / second mitotic wave involved in compound eye morphogenesis ...larval salivary gland morphogenesis / Pre-NOTCH Processing in Golgi / NOTCH4 Activation and Transmission of Signal to the Nucleus / Negative regulation of NOTCH4 signaling / eye-antennal disc development / crystal cell differentiation / negative regulation of lamellocyte differentiation / cuticle pattern formation / lateral inhibition / second mitotic wave involved in compound eye morphogenesis / imaginal disc-derived wing margin morphogenesis / imaginal disc-derived leg segmentation / imaginal disc-derived leg morphogenesis / wing disc anterior/posterior pattern formation / larval lymph gland hemopoiesis / compound eye development / imaginal disc-derived wing morphogenesis / glycosphingolipid binding / apical cortex / sensory organ development / germ-line stem cell population maintenance / Notch binding / axolemma / salivary gland morphogenesis / glial cell proliferation / Notch signaling pathway / apical plasma membrane / receptor ligand activity / calcium ion binding / cell surface / plasma membrane
Similarity search - Function
: / Jagged/Serrate protein / Immunoglobulin-like - #3510 / 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 ...: / Jagged/Serrate protein / Immunoglobulin-like - #3510 / 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 / von Willebrand factor (vWF) type C domain / VWFC domain / : / 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. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 7, 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
Revision 1.3Oct 16, 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

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Assembly

Deposited unit
A: Protein serrate
B: Protein serrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1687
Polymers59,2212
Non-polymers9475
Water2,126118
1
A: Protein serrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0753
Polymers29,6111
Non-polymers4642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein serrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0934
Polymers29,6111
Non-polymers4823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.329, 49.402, 93.123
Angle α, β, γ (deg.)90.000, 110.249, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 80 through 191 or resid 196 through 348 or resid 1 through 2))
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALATYRA1 - 112
d_12ens_1PROLEUA117 - 269
d_13ens_1NAGNAGB
d_14ens_1NAGNAGC
d_21ens_1ALALEUD1 - 265
d_22ens_1NAGNAGE
d_23ens_1NAGNAGF

NCS oper: (Code: givenMatrix: (-0.999906210829, -0.000599648350543, 0.0136824693301), (-0.000858325876441, 0.999820864457, -0.0189077304919), (-0.0136686803242, -0.0189177011691, -0.999727606781) ...NCS oper: (Code: given
Matrix: (-0.999906210829, -0.000599648350543, 0.0136824693301), (-0.000858325876441, 0.999820864457, -0.0189077304919), (-0.0136686803242, -0.0189177011691, -0.999727606781)
Vector: 54.2122919255, 2.45690748875, 44.021735424)

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Components

#1: Protein Protein serrate / Protein beaded


Mass: 29610.537 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Ser, Bd, CG6127 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P18168
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.1M imidazole malate pH 7, 25% PEG4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.03→45.61 Å / Num. obs: 38729 / % possible obs: 98.89 % / Redundancy: 3.3 % / Biso Wilson estimate: 31.49 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.1
Reflection shellResolution: 2.03→2.103 Å / Num. unique obs: 3814 / CC1/2: 0.769

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Processing

Software
NameVersionClassification
PHENIXdev_3965refinement
PHENIXdev_3965refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MW7

5mw7


Resolution: 2.03→45.61 Å / SU ML: 0.2152 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3516
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2579 1996 5.15 %
Rwork0.22 36733 -
obs0.222 38729 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.24 Å2
Refinement stepCycle: LAST / Resolution: 2.03→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4079 0 58 118 4255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00524229
X-RAY DIFFRACTIONf_angle_d0.81115738
X-RAY DIFFRACTIONf_chiral_restr0.0774634
X-RAY DIFFRACTIONf_plane_restr0.0054742
X-RAY DIFFRACTIONf_dihedral_angle_d9.9097601
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.92239358248 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.080.34081330.32952588X-RAY DIFFRACTION98.34
2.08-2.140.32461420.28172619X-RAY DIFFRACTION99.39
2.14-2.20.28491450.27182611X-RAY DIFFRACTION99.57
2.2-2.270.28661320.2782597X-RAY DIFFRACTION98.13
2.27-2.350.26491690.24352593X-RAY DIFFRACTION99.86
2.35-2.450.27151290.24292649X-RAY DIFFRACTION99.39
2.45-2.560.27781350.23892609X-RAY DIFFRACTION99.35
2.56-2.690.28791540.24152621X-RAY DIFFRACTION99.18
2.69-2.860.2781390.24242617X-RAY DIFFRACTION99.35
2.86-3.080.3021340.23192665X-RAY DIFFRACTION99.08
3.08-3.390.27571340.22312597X-RAY DIFFRACTION98.45
3.39-3.880.23631690.1992612X-RAY DIFFRACTION98.13
3.88-4.890.19211180.16482648X-RAY DIFFRACTION98.02
4.89-45.610.24521630.20642707X-RAY DIFFRACTION98.52

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