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- PDB-4xbm: X-ray crystal structure of Notch ligand Delta-like 1 -

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Basic information

Entry
Database: PDB / ID: 4xbm
TitleX-ray crystal structure of Notch ligand Delta-like 1
ComponentsDelta-like protein 1
KeywordsSIGNALING PROTEIN / ectodomain EGF-like repeat Ligand C2 domain
Function / homology
Function and homology information


cerebellar molecular layer formation / regulation of skeletal muscle tissue growth / Notch signaling pathway involved in arterial endothelial cell fate commitment / skin epidermis development / proximal tubule development / negative regulation of epidermal cell differentiation / regulation of vascular endothelial growth factor signaling pathway / somite specification / lateral inhibition / loop of Henle development ...cerebellar molecular layer formation / regulation of skeletal muscle tissue growth / Notch signaling pathway involved in arterial endothelial cell fate commitment / skin epidermis development / proximal tubule development / negative regulation of epidermal cell differentiation / regulation of vascular endothelial growth factor signaling pathway / somite specification / lateral inhibition / loop of Henle development / skeletal muscle tissue growth / retina morphogenesis in camera-type eye / endothelial tip cell fate specification / MECP2 regulates transcription of neuronal ligands / nephron development / cerebellar Purkinje cell layer structural organization / negative regulation of cardiac muscle cell differentiation / marginal zone B cell differentiation / negative regulation of inner ear auditory receptor cell differentiation / regulation of somitogenesis / positive regulation of skeletal muscle tissue growth / neuron fate specification / compartment pattern specification / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / negative regulation of myeloid cell differentiation / negative regulation of glial cell apoptotic process / left/right axis specification / proximal/distal pattern formation / type B pancreatic cell development / neuronal stem cell population maintenance / Tat protein binding / astrocyte development / clathrin-dependent endocytosis / cell fate determination / negative regulation of myoblast differentiation / Notch binding / determination of left/right symmetry / regulation of growth / negative regulation of epithelial cell differentiation / organ growth / spinal cord development / negative regulation of interleukin-10 production / positive regulation of endocytosis / positive regulation of Notch signaling pathway / regulation of cell division / heart looping / negative regulation of Notch signaling pathway / positive regulation of sprouting angiogenesis / plasma membrane => GO:0005886 / inner ear development / negative regulation of cell differentiation / hemopoiesis / negative regulation of neuron differentiation / regulation of neurogenesis / somitogenesis / regulation of cell adhesion / energy homeostasis / Notch signaling pathway / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / NOTCH3 Activation and Transmission of Signal to the Nucleus / adherens junction / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / regulation of blood pressure / retina development in camera-type eye / cytoplasmic vesicle / scaffold protein binding / cell differentiation / membrane raft / apical plasma membrane / negative regulation of cell population proliferation / calcium ion binding / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / extracellular region / plasma membrane
Similarity search - Function
Laminin - #140 / 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 / EGF-like, conserved site / Human growth factor-like EGF ...Laminin - #140 / 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 / EGF-like, conserved site / Human growth factor-like EGF / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / 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 / Ribbon / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-L-fucopyranose / Delta-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsKershaw, N.J. / Burgess, A.W. / Church, N.L. / Luo, C.S. / Adam, T.E.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)487922 Australia
CitationJournal: Biochem.J. / Year: 2015
Title: Notch ligand delta-like1: X-ray crystal structure and binding affinity.
Authors: Kershaw, N.J. / Church, N.L. / Griffin, M.D. / Luo, C.S. / Adams, T.E. / Burgess, A.W.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2May 27, 2015Group: Data collection / Structure summary
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity / entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity.src_method / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Delta-like protein 1
B: Delta-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,0263
Polymers114,8622
Non-polymers1641
Water0
1
A: Delta-like protein 1


Theoretical massNumber of molelcules
Total (without water)57,4311
Polymers57,4311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Delta-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5952
Polymers57,4311
Non-polymers1641
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.150, 118.870, 134.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Delta-like protein 1 / Drosophila Delta homolog 1 / H-Delta-1


Mass: 57430.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLL1, UNQ146/PRO172 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: O00548
#2: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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

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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: 3.77 Å3/Da / Density % sol: 67.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.4M potassium thiocyanate 16% PEG3350 0.1M Bis-tris propane pH 7.5 5mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.2→67.4 Å / Num. obs: 29271 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.432 / Net I/σ(I): 6.27
Reflection shellResolution: 3.2→3.314 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
PHASERphasing
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CBZ

4cbz


Resolution: 3.2→67.3 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2835 1997 6.83 %
Rwork0.2584 --
obs0.2601 29260 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→67.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4987 0 10 0 4997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045176
X-RAY DIFFRACTIONf_angle_d0.9286964
X-RAY DIFFRACTIONf_dihedral_angle_d11.7281857
X-RAY DIFFRACTIONf_chiral_restr0.036699
X-RAY DIFFRACTIONf_plane_restr0.007929
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.31440.37711960.36672675X-RAY DIFFRACTION100
3.3144-3.44710.39541950.34372673X-RAY DIFFRACTION100
3.4471-3.6040.3421990.32072706X-RAY DIFFRACTION100
3.604-3.7940.30561960.2892675X-RAY DIFFRACTION100
3.794-4.03160.30041980.27132725X-RAY DIFFRACTION100
4.0316-4.34290.27961980.24222710X-RAY DIFFRACTION100
4.3429-4.77980.23951990.20852708X-RAY DIFFRACTION100
4.7798-5.47120.22722010.20312736X-RAY DIFFRACTION100
5.4712-6.8920.25772020.24842774X-RAY DIFFRACTION100
6.892-67.30.28852130.26152881X-RAY DIFFRACTION99

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