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- PDB-5mvx: Human DLL4 C2-EGF3 -

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Basic information

Entry
Database: PDB / ID: 5mvx
TitleHuman DLL4 C2-EGF3
ComponentsDelta-like protein 4
KeywordsSIGNALING PROTEIN / C2 / EGF / Notch / signaling
Function / homology
Function and homology information


ventral spinal cord interneuron fate commitment / regulation of neural retina development / Notch signaling involved in heart development / blood vessel lumenization / dorsal aorta morphogenesis / cardiac ventricle morphogenesis / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / NOTCH4 Activation and Transmission of Signal to the Nucleus / pericardium morphogenesis ...ventral spinal cord interneuron fate commitment / regulation of neural retina development / Notch signaling involved in heart development / blood vessel lumenization / dorsal aorta morphogenesis / cardiac ventricle morphogenesis / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / NOTCH4 Activation and Transmission of Signal to the Nucleus / pericardium morphogenesis / cardiac atrium morphogenesis / ventricular trabecula myocardium morphogenesis / negative regulation of cell migration involved in sprouting angiogenesis / positive regulation of neural precursor cell proliferation / cellular response to fibroblast growth factor stimulus / aortic valve morphogenesis / blood circulation / Notch binding / negative regulation of endothelial cell migration / branching involved in blood vessel morphogenesis / positive regulation of Notch signaling pathway / negative regulation of Notch signaling pathway / T cell differentiation / regulation of neurogenesis / cellular response to vascular endothelial growth factor stimulus / blood vessel remodeling / Notch signaling pathway / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / visual perception / Activated NOTCH1 Transmits Signal to the Nucleus / NOTCH3 Activation and Transmission of Signal to the Nucleus / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / angiogenesis / membrane => GO:0016020 / negative regulation of cell population proliferation / negative regulation of gene expression / calcium ion binding / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / signal transduction / 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 / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain ...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 domain / EGF-type aspartate/asparagine hydroxylation site / 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
alpha-L-fucopyranose / Delta-like protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsSuckling, R.J. / Handford, P.A. / Lea, S.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/L001187/1 United Kingdom
CitationJournal: EMBO J. / Year: 2017
Title: Structural and functional dissection of the interplay between lipid and Notch binding by human Notch ligands.
Authors: Suckling, R.J. / Korona, B. / Whiteman, P. / Chillakuri, C. / Holt, L. / Handford, P.A. / Lea, S.M.
History
DepositionJan 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 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 1.4Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: Delta-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3962
Polymers34,2321
Non-polymers1641
Water3,531196
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint4 kcal/mol
Surface area18110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.896, 49.753, 70.031
Angle α, β, γ (deg.)90.00, 109.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Delta-like protein 4 / Drosophila Delta homolog 4 / Delta4


Mass: 34232.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLL4, UNQ1895/PRO4341 / Plasmid: pEXS2-2 / Cell (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q9NR61
#2: 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: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 20K, MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.17→66.2 Å / Num. obs: 21802 / % possible obs: 98 % / Redundancy: 4.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Net I/σ(I): 14.6
Reflection shellResolution: 2.17→2.24 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.508 / CC1/2: 0.852 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CC1

4cc1


Resolution: 2.17→66.155 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.3
RfactorNum. reflection% reflection
Rfree0.2293 1092 5.01 %
Rwork0.1823 --
obs0.1847 21802 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.5 Å2
Refinement stepCycle: LAST / Resolution: 2.17→66.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 10 196 2507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052403
X-RAY DIFFRACTIONf_angle_d0.8123280
X-RAY DIFFRACTIONf_dihedral_angle_d14.1391443
X-RAY DIFFRACTIONf_chiral_restr0.048338
X-RAY DIFFRACTIONf_plane_restr0.005435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1701-2.26880.28751260.24982457X-RAY DIFFRACTION93
2.2688-2.38850.32631490.22812585X-RAY DIFFRACTION98
2.3885-2.53810.25681170.22132599X-RAY DIFFRACTION98
2.5381-2.73410.28171440.22112581X-RAY DIFFRACTION99
2.7341-3.00920.28261210.2142580X-RAY DIFFRACTION98
3.0092-3.44460.23751380.192629X-RAY DIFFRACTION99
3.4446-4.33980.21381390.15842602X-RAY DIFFRACTION98
4.3398-66.1860.18471580.1582677X-RAY DIFFRACTION99

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