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- PDB-4l0p: Structure of the human EphA3 receptor ligand binding domain compl... -

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Basic information

Entry
Database: PDB / ID: 4l0p
TitleStructure of the human EphA3 receptor ligand binding domain complexed with ephrin-A5
Components
  • Ephrin type-A receptor 3
  • Ephrin-A5
KeywordsTRANSFERASE/TRANSFERASE RECEPTOR / beta-sandwich / Receptor Tyrosine Kinase / ephrin binding / TRANSFERASE-TRANSFERASE RECEPTOR complex
Function / homology
Function and homology information


neurotrophin TRKC receptor binding / neurotrophin TRKB receptor binding / fasciculation of sensory neuron axon / fasciculation of motor neuron axon / negative regulation of substrate adhesion-dependent cell spreading / transmembrane-ephrin receptor activity / synaptic membrane adhesion / GPI-linked ephrin receptor activity / regulation of epithelial to mesenchymal transition / collateral sprouting ...neurotrophin TRKC receptor binding / neurotrophin TRKB receptor binding / fasciculation of sensory neuron axon / fasciculation of motor neuron axon / negative regulation of substrate adhesion-dependent cell spreading / transmembrane-ephrin receptor activity / synaptic membrane adhesion / GPI-linked ephrin receptor activity / regulation of epithelial to mesenchymal transition / collateral sprouting / positive regulation of collateral sprouting / cellular response to follicle-stimulating hormone stimulus / regulation of insulin secretion involved in cellular response to glucose stimulus / ephrin receptor activity / negative regulation of endocytosis / neurotrophin TRKA receptor binding / chemorepellent activity / regulation of cell morphogenesis / positive regulation of synapse assembly / EPH-Ephrin signaling / regulation of focal adhesion assembly / regulation of GTPase activity / retinal ganglion cell axon guidance / EPHA-mediated growth cone collapse / transmembrane receptor protein tyrosine kinase activator activity / regulation of cell-cell adhesion / basement membrane / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / regulation of microtubule cytoskeleton organization / GABA-ergic synapse / cellular response to forskolin / cellular response to retinoic acid / ephrin receptor binding / axon guidance / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / adherens junction / receptor protein-tyrosine kinase / caveola / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / positive regulation of peptidyl-tyrosine phosphorylation / cell migration / actin cytoskeleton / nervous system development / nuclear membrane / early endosome / cell adhesion / positive regulation of protein phosphorylation / external side of plasma membrane / dendrite / extracellular region / nucleoplasm / ATP binding / plasma membrane / cytosol
Similarity search - Function
Ephrin-A ectodomain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Ephrin type-A receptor 3, ligand binding domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like ...Ephrin-A ectodomain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Ephrin type-A receptor 3, 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 / Cupredoxins - blue copper proteins / Sterile alpha motif/pointed domain superfamily / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / Fibronectin type III domain / Cupredoxin / 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 / Jelly Rolls / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ephrin type-A receptor 3 / Ephrin-A5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsForse, G.J. / Kolatkar, A.R. / Kuhn, P.
CitationJournal: Plos One / Year: 2015
Title: Distinctive Structure of the EphA3/Ephrin-A5 Complex Reveals a Dual Mode of Eph Receptor Interaction for Ephrin-A5.
Authors: Forse, G.J. / Uson, M.L. / Nasertorabi, F. / Kolatkar, A. / Lamberto, I. / Pasquale, E.B. / Kuhn, P.
History
DepositionMay 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Other
Revision 1.2Jul 1, 2015Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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: Ephrin type-A receptor 3
B: Ephrin-A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9259
Polymers36,9812
Non-polymers9457
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-73 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.043, 60.043, 91.574
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Ephrin type-A receptor 3 / EPH-like kinase 4 / EK4 / hEK4 / HEK / Human embryo kinase / Tyrosine-protein kinase TYRO4 / ...EPH-like kinase 4 / EK4 / hEK4 / HEK / Human embryo kinase / Tyrosine-protein kinase TYRO4 / Tyrosine-protein kinase receptor ETK1 / Eph-like tyrosine kinase 1


Mass: 20258.836 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain (UNP residues 29-201)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA3, EPHA3_HUMAN, ETK, ETK1, HEK, TYRO4 / Plasmid: pET32b / Production host: Escherichia coli (E. coli) / References: UniProt: P29320
#2: Protein Ephrin-A5 / AL-1 / EPH-related receptor tyrosine kinase ligand 7 / LERK-7


Mass: 16721.770 Da / Num. of mol.: 1 / Fragment: Receptor Binding Domain (UNP residues 27-166)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EFNA5, EFNA5_HUMAN, EPLG7, LERK7 / Plasmid: pFASTBAC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P52803

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Sugars , 1 types, 1 molecules

#3: 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

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Non-polymers , 3 types, 113 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.05M ammonium sulphate, 0.1M tris, 5mM calcium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 21, 2012 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 15094 / % possible obs: 98.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 27.87 Å2 / Rmerge(I) obs: 0.19 / Rsym value: 0.19 / Net I/σ(I): 7.9
Reflection shellResolution: 2.26→2.34 Å / Redundancy: 4 % / Rmerge(I) obs: 0.839 / Mean I/σ(I) obs: 1.6 / % possible all: 97.6

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
AutoSolphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The ephrin-A5 subunit from PDB entry 1SHW

1shw


Resolution: 2.26→38.518 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2111 778 5.17 %
Rwork0.1866 --
obs0.1879 15050 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→38.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2576 0 54 107 2737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042703
X-RAY DIFFRACTIONf_angle_d0.7853656
X-RAY DIFFRACTIONf_dihedral_angle_d13.367985
X-RAY DIFFRACTIONf_chiral_restr0.052378
X-RAY DIFFRACTIONf_plane_restr0.003469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.39810.29871370.282303X-RAY DIFFRACTION95
2.3981-2.58330.28751250.24212366X-RAY DIFFRACTION98
2.5833-2.84320.25791400.21472381X-RAY DIFFRACTION99
2.8432-3.25440.21271140.19122421X-RAY DIFFRACTION99
3.2544-4.09950.18141270.15312380X-RAY DIFFRACTION99
4.0995-38.52390.16481350.15882421X-RAY DIFFRACTION98
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)
11.6825-1.73810.2951.5104-0.16235.0147-0.1687-0.1294-0.02770.08930.1245-0.1979-0.14170.23350.00440.24210.0006-0.02050.2113-0.01350.276685.087540.40879.7767
21.6823-0.5164-1.64221.64721.05825.07760.1005-0.3736-0.0397-0.0894-0.0593-0.1448-0.08320.5712-0.01990.2089-0.0135-0.05950.21980.02390.188879.48251.51825.8128
34.1170.18660.20550.79160.68952.73770.32590.0921-0.1295-0.4982-0.238-0.12360.09590.3157-0.0320.2489-0.03770.03860.2177-0.03320.230785.989144.7529-3.1579
42.3744-3.08190.55056.2811-1.36590.56530.07630.3619-0.1858-0.4462-0.06280.36330.10610.08310.03010.315-0.0546-0.03260.2403-0.01380.238372.456848.3225-4.7786
53.0759-1.1810.38212.73340.00252.38360.12310.05810.1821-0.1998-0.0359-0.3848-0.07250.4647-0.05870.2549-0.00810.03140.3473-0.00840.239288.618440.2833-6.3279
65.1634-2.8916-2.63295.30045.68498.12920.09860.03250.0346-0.1954-0.01140.6237-0.2254-0.34740.02950.2379-0.01570.00830.27480.06480.305462.806352.72161.172
71.3382-0.6418-0.36442.39250.2061.2975-0.08190.1482-0.24760.05670.05780.09670.05780.06440.03440.2212-0.0410.00220.2134-0.02850.250780.628738.14510.4138
82.4088-0.60231.83342.7451-2.2292.9340.0283-0.02770.22770.3227-0.1458-0.3014-0.46450.37730.07040.2954-0.0927-0.03220.21810.01920.268784.74767.271115.4073
92.0213-9.2994-2.77738.29664.39172.0296-0.7394-0.4648-0.48981.14620.40660.0387-0.1005-0.33340.31040.6216-0.0422-0.07220.49410.0870.372788.318152.196634.2575
100.9085-1.5568-0.18844.5686-1.74583.3577-0.227-0.2730.02160.82280.54120.2513-1.128-0.5793-0.25480.48670.03440.09020.32530.04320.294872.144764.78422.5036
110.39570.19120.23641.3783-1.41773.6426-0.00130.01890.0490.1239-0.0341-0.0199-0.10840.01660.0160.19420.0248-0.01080.2022-0.01190.230876.505958.305411.9153
123.2393-2.98744.01059.0153-8.23622.26040.0778-0.3547-0.1680.73430.17590.4103-0.9242-0.4991-0.08770.2389-0.03190.00930.2473-0.02390.210972.946865.950518.6815
130.76970.2672-1.840.0856-0.62554.39370.1027-0.95440.10381.13540.89761.5689-0.8741-0.759-0.82620.70320.23270.11270.63050.05520.844372.088468.175831.1127
142.04580.1176-1.11165.5739-5.06492.08890.3636-0.00890.39360.064-0.0868-0.037-0.37860.8192-0.05140.279-0.0248-0.03950.2275-0.02080.32179.14474.11936.1906
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 27:46)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 47:70)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 71:93)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 94:117)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 118:147)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 148:161)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 162:201)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 27:65)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 66:72)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 73:93)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 94:133)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 134:145)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 146:151)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 152:165)

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