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- PDB-4w50: Structure of the EphA4 LBD in complex with peptide -

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Basic information

Entry
Database: PDB / ID: 4w50
TitleStructure of the EphA4 LBD in complex with peptide
Components
  • APY peptide
  • Ephrin type-A receptor 4
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Protein-Inhibitor Complex / Ligand Binding Domain / Signal Transduction / Receptor-Tyrosine Kinase / Cyclic Peptide / EphA4 / Phage Display / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


DH domain binding / neuron projection fasciculation / positive regulation of Rho guanyl-nucleotide exchange factor activity / corticospinal tract morphogenesis / regulation of astrocyte differentiation / negative regulation of proteolysis involved in protein catabolic process / neuron projection guidance / nephric duct morphogenesis / fasciculation of sensory neuron axon / fasciculation of motor neuron axon ...DH domain binding / neuron projection fasciculation / positive regulation of Rho guanyl-nucleotide exchange factor activity / corticospinal tract morphogenesis / regulation of astrocyte differentiation / negative regulation of proteolysis involved in protein catabolic process / neuron projection guidance / nephric duct morphogenesis / fasciculation of sensory neuron axon / fasciculation of motor neuron axon / regulation of synapse pruning / synapse pruning / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / negative regulation of cellular response to hypoxia / negative regulation of axon regeneration / glial cell migration / PH domain binding / GPI-linked ephrin receptor activity / regulation of modification of synaptic structure / regulation of dendritic spine morphogenesis / transmembrane-ephrin receptor activity / negative regulation of cell adhesion / negative regulation of epithelial to mesenchymal transition / adult walking behavior / motor neuron axon guidance / adherens junction organization / positive regulation of dendrite morphogenesis / EPH-Ephrin signaling / Somitogenesis / positive regulation of amyloid-beta formation / regulation of axonogenesis / cochlea development / regulation of GTPase activity / EPHA-mediated growth cone collapse / positive regulation of protein tyrosine kinase activity / positive regulation of cell adhesion / 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 / negative regulation of cell migration / protein tyrosine kinase binding / dendritic shaft / filopodium / adherens junction / postsynaptic density membrane / axon guidance / Schaffer collateral - CA1 synapse / neuromuscular junction / receptor protein-tyrosine kinase / negative regulation of ERK1 and ERK2 cascade / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / negative regulation of neuron projection development / presynaptic membrane / kinase activity / amyloid-beta binding / early endosome membrane / perikaryon / protein tyrosine kinase activity / mitochondrial outer membrane / protein autophosphorylation / dendritic spine / protein stabilization / negative regulation of translation / cell adhesion / protein kinase activity / positive regulation of cell migration / axon / glutamatergic synapse / dendrite / positive regulation of cell population proliferation / 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 2 transmembrane 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) / Galactose-binding domain-like / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Jelly Rolls / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
1,3-BUTANEDIOL / Ephrin type-A receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.42 Å
AuthorsLechtenberg, B.C. / Mace, P.D. / Riedl, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01CA138390 United States
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Development and Structural Analysis of a Nanomolar Cyclic Peptide Antagonist for the EphA4 Receptor.
Authors: Lamberto, I. / Lechtenberg, B.C. / Olson, E.J. / Mace, P.D. / Dawson, P.E. / Riedl, S.J. / Pasquale, E.B.
History
DepositionAug 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Jan 14, 2015Group: Data collection
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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: Ephrin type-A receptor 4
C: Ephrin type-A receptor 4
D: Ephrin type-A receptor 4
E: APY peptide
F: APY peptide
G: APY peptide
H: APY peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,44018
Polymers87,5278
Non-polymers91310
Water3,171176
1
A: Ephrin type-A receptor 4
E: APY peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2486
Polymers21,8822
Non-polymers3664
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-8 kcal/mol
Surface area10030 Å2
MethodPISA
2
B: Ephrin type-A receptor 4
F: APY peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0644
Polymers21,8822
Non-polymers1822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-6 kcal/mol
Surface area10180 Å2
MethodPISA
3
C: Ephrin type-A receptor 4
G: APY peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0644
Polymers21,8822
Non-polymers1822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-11 kcal/mol
Surface area9780 Å2
MethodPISA
4
D: Ephrin type-A receptor 4
H: APY peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0644
Polymers21,8822
Non-polymers1822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-7 kcal/mol
Surface area9860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.270, 127.690, 84.569
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Detailschains A+E / chains B+F / chains C+G / chains D+H

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Components

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


Mass: 20489.143 Da / Num. of mol.: 4 / Fragment: ligand binding domain, UNP residues 29-204 / Mutation: C204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA4, HEK8, SEK, TYRO1 / Plasmid: NKI His-3C-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2
References: UniProt: P54764, receptor protein-tyrosine kinase
#2: Protein/peptide
APY peptide


Mass: 1392.583 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-BU2 / 1,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M MgCl2, 0.1M Tris pH8.5, 25% PEG3350, 4% 1,3-butanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.664
11-h,-k,l20.336
ReflectionResolution: 2.42→50.95 Å / Num. obs: 27280 / % possible obs: 93.4 % / Redundancy: 6.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.034 / Net I/σ(I): 14.4 / Num. measured all: 179142 / Scaling rejects: 54
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.42-2.526.30.2464.91817228820.9710.10490.1
8.72-50.957.10.06623.846276560.9890.02799.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.51 Å50.95 Å
Translation3.51 Å50.95 Å

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOSFLMdata reduction
Aimless0.2.1data scaling
PHASER2.5.4phasing
REFMAC5.8.0071refinement
Coot0.7.2model building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WO1

2wo1


Resolution: 2.42→50.95 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.2401 / WRfactor Rwork: 0.1757 / FOM work R set: 0.7586 / SU B: 19.791 / SU ML: 0.226 / SU R Cruickshank DPI: 0.2951 / SU Rfree: 0.0614 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.295 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2325 1346 4.9 %RANDOM
Rwork0.1706 25907 --
obs0.1735 27253 92.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 109.63 Å2 / Biso mean: 43.273 Å2 / Biso min: 22.14 Å2
Baniso -1Baniso -2Baniso -3
1--4.62 Å20 Å216.89 Å2
2--27.25 Å20 Å2
3----22.63 Å2
Refinement stepCycle: final / Resolution: 2.42→50.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6090 0 60 176 6326
Biso mean--56.04 38.69 -
Num. residues----756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.026276
X-RAY DIFFRACTIONr_bond_other_d0.0010.025856
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9538484
X-RAY DIFFRACTIONr_angle_other_deg0.734313456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7965746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.64124.103312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.947151080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8991548
X-RAY DIFFRACTIONr_chiral_restr0.080.2916
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027070
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021474
X-RAY DIFFRACTIONr_mcbond_it0.9212.6053010
X-RAY DIFFRACTIONr_mcbond_other0.9212.6053009
X-RAY DIFFRACTIONr_mcangle_it1.6453.93750
LS refinement shellResolution: 2.42→2.482 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 95 -
Rwork0.301 1765 -
all-1860 -
obs--89.34 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.103-0.2431-0.81470.99890.39042.78760.0002-0.052-0.02660.04640.0535-0.02540.14890.1092-0.05380.25140.0128-0.19690.0082-0.00750.1558-5.867-18.3155-5.705
21.1236-0.1613-0.0540.8728-0.56862.95320.0555-0.038-0.0589-0.00520.02380.0025-0.1868-0.1191-0.07930.21040.0298-0.15920.0092-0.01450.1414-6.62441.411136.7358
31.4261-0.46580.27231.6907-0.3162.77250.12380.0532-0.016-0.1939-0.158-0.03260.2854-0.03610.03420.22870.0229-0.16050.0171-0.00720.15294.5702-27.024638.5232
41.8098-0.5838-0.98041.49040.11933.28340.1501-0.06820.073-0.1452-0.04790.0036-0.3987-0.1111-0.10220.22230.0211-0.14180.0156-0.00290.1491-16.722810.34-3.5005
50.0234-0.0894-0.017.583-3.86548.00050.0378-0.0252-0.0377-0.5107-0.04580.1470.0937-0.1010.0080.0951-0.0142-0.07020.08010.02540.0672-7.6074-23.4177-22.2079
60.429-1.2534-0.72637.3632-0.38623.02310.1354-0.04270.0125-0.1475-0.0655-0.0597-0.34030.1661-0.070.1920.0457-0.0220.11510.03750.0466-16.523417.1385-19.6639
73.40380.92070.098512.6611-2.80240.64970.15740.2433-0.118-0.3656-0.15240.00920.10250.0495-0.0050.17590.0645-0.00940.1191-0.05270.03684.0521-33.468822.4825
86.72911.9302-2.41277.87094.32274.3418-0.01520.3199-0.0001-0.22030.1236-0.2063-0.1502-0.0258-0.10840.1719-0.0004-0.08190.12670.0490.0756-4.8326.7120.2406
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 204
2X-RAY DIFFRACTION2B28 - 204
3X-RAY DIFFRACTION3C28 - 204
4X-RAY DIFFRACTION4D28 - 204
5X-RAY DIFFRACTION5E1 - 12
6X-RAY DIFFRACTION6F1 - 12
7X-RAY DIFFRACTION7G1 - 12
8X-RAY DIFFRACTION8H1 - 12

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