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- PDB-9cy8: Constrained b-hairpins targeting the EphA4 ligand binding domain -

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Basic information

Entry
Database: PDB / ID: 9cy8
TitleConstrained b-hairpins targeting the EphA4 ligand binding domain
Components
  • Constrained b-hairpin
  • Ephrin type-A receptor 4
KeywordsLIPID BINDING PROTEIN / receptor tyrosine kinase EphA4
Function / homology
Function and homology information


DH domain binding / neuron projection fasciculation / : / negative regulation of proteolysis involved in protein catabolic process / corticospinal tract morphogenesis / regulation of astrocyte differentiation / neuron projection guidance / nephric duct morphogenesis / fasciculation of sensory neuron axon / fasciculation of motor neuron axon ...DH domain binding / neuron projection fasciculation / : / negative regulation of proteolysis involved in protein catabolic process / corticospinal tract morphogenesis / regulation of astrocyte differentiation / neuron projection guidance / nephric duct morphogenesis / fasciculation of sensory neuron axon / fasciculation of motor neuron axon / synapse pruning / negative regulation of cellular response to hypoxia / negative regulation of axon regeneration / glial cell migration / positive regulation of amyloid precursor protein catabolic process / PH domain binding / regulation of modification of synaptic structure / regulation of synapse pruning / regulation of dendritic spine morphogenesis / positive regulation of dendrite morphogenesis / negative regulation of cell adhesion / innervation / adherens junction organization / motor neuron axon guidance / EPH-Ephrin signaling / adult walking behavior / regulation of GTPase activity / negative regulation of epithelial to mesenchymal transition / Somitogenesis / positive regulation of amyloid-beta formation / regulation of axonogenesis / EPHA-mediated growth cone collapse / cochlea development / positive regulation of intracellular signal transduction / negative regulation of long-term synaptic potentiation / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / axonal growth cone / axon terminus / ephrin receptor binding / positive regulation of cell adhesion / axon guidance / dendritic shaft / negative regulation of cell migration / protein tyrosine kinase binding / filopodium / adherens junction / placental growth factor receptor activity / postsynaptic density membrane / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / negative regulation of ERK1 and ERK2 cascade / receptor protein-tyrosine kinase / neuromuscular junction / peptidyl-tyrosine phosphorylation / Schaffer collateral - CA1 synapse / cellular response to amyloid-beta / kinase activity / amyloid-beta binding / presynaptic membrane / negative regulation of neuron projection development / protein autophosphorylation / protein tyrosine kinase activity / early endosome membrane / dendritic spine / perikaryon / negative regulation of neuron apoptotic process / mitochondrial outer membrane / protein kinase activity / negative regulation of translation / cell adhesion / protein stabilization / positive regulation of cell migration / axon / positive regulation of cell population proliferation / dendrite / glutamatergic synapse / cell surface / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Ephrin type-A receptor 4, SAM domain / Ephrin type-A receptor 4, ligand binding domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / : / Ephrin receptor ligand binding domain ...Ephrin type-A receptor 4, SAM domain / Ephrin type-A receptor 4, ligand binding domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / : / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. / Ephrin receptor ligand binding domain / Putative ephrin-receptor like / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Ephrin type-A receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMuzzarelli, K.M. / Assar, Z. / Prentis, A.M. / Baggio, C. / Pellecchia, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: Constrained beta-Hairpins Targeting the EphA4 Ligand Binding Domain.
Authors: Prentiss, A.M. / Baggio, C. / Pagett, J. / Kulinich, A.O. / Ethell, I.M. / Muzzarelli, K. / Assar, Z. / Pellecchia, M.
History
DepositionAug 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ephrin type-A receptor 4
B: Constrained b-hairpin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8133
Polymers22,7782
Non-polymers351
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-18 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.059, 128.053, 34.907
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-422-

HOH

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Components

#1: Protein Ephrin type-A receptor 4 / EPH-like kinase 8 / EK8 / hEK8 / Tyrosine-protein kinase TYRO1 / Tyrosine-protein kinase receptor SEK


Mass: 21259.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA4, HEK8, SEK, TYRO1 / Production host: Escherichia coli (E. coli)
References: UniProt: P54764, receptor protein-tyrosine kinase
#2: Protein/peptide Constrained b-hairpin


Mass: 1518.737 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Citric acid, pH 3.5, and 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.953 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.5→36.15 Å / Num. obs: 15002 / % possible obs: 99.8 % / Redundancy: 8 % / Biso Wilson estimate: 47.19 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1754 / Net I/σ(I): 10.6
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 669 / CC1/2: 0.901

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→36.15 Å / SU ML: 0.265 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6928
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2568 453 4.94 %
Rwork0.2132 8718 -
obs0.2155 9171 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.11 Å2
Refinement stepCycle: LAST / Resolution: 2.5→36.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1460 0 47 51 1558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00581536
X-RAY DIFFRACTIONf_angle_d0.69912073
X-RAY DIFFRACTIONf_chiral_restr0.0477222
X-RAY DIFFRACTIONf_plane_restr0.0037264
X-RAY DIFFRACTIONf_dihedral_angle_d13.0328568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.860.30481450.26952833X-RAY DIFFRACTION99.73
2.86-3.60.24491440.22452867X-RAY DIFFRACTION100
3.61-36.150.25031640.19433018X-RAY DIFFRACTION99.87

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