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- PDB-3p1i: Ligand binding domain of human ephrin type-B receptor 3 -

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Basic information

Entry
Database: PDB / ID: 3p1i
TitleLigand binding domain of human ephrin type-B receptor 3
ComponentsEphrin type-B receptor 3
KeywordsTRANSFERASE / SIGNALING PROTEIN / ATP-binding / kinase / nucleotide-binding / receptor / phosphorylation / transmembrane / tyrosine-protein kinase / glycoprotein / Structural Genomics Consortium / SGC / membrane / Single-pass type I membrane protein
Function / homology
Function and homology information


urogenital system development / axon guidance receptor activity / central nervous system projection neuron axonogenesis / regulation of cell-cell adhesion / transmembrane-ephrin receptor activity / dendritic spine development / corpus callosum development / ephrin receptor activity / dendritic spine morphogenesis / retinal ganglion cell axon guidance ...urogenital system development / axon guidance receptor activity / central nervous system projection neuron axonogenesis / regulation of cell-cell adhesion / transmembrane-ephrin receptor activity / dendritic spine development / corpus callosum development / ephrin receptor activity / dendritic spine morphogenesis / retinal ganglion cell axon guidance / axonal fasciculation / positive regulation of synapse assembly / EPH-Ephrin signaling / Ephrin signaling / digestive tract morphogenesis / regulation of axonogenesis / regulation of GTPase activity / roof of mouth development / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / EPHB-mediated forward signaling / substrate adhesion-dependent cell spreading / thymus development / axon guidance / receptor protein-tyrosine kinase / cell migration / angiogenesis / protein autophosphorylation / dendrite / extracellular region / ATP binding / plasma membrane / cytosol
Similarity search - Function
Ephrin type-B 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. ...Ephrin type-B 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 / 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 / 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
Ephrin type-B receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWalker, J.R. / Yermekbayeva, L. / Seitova, A. / Kania, J. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Ligand Binding Domain of Human Ephb3
Authors: Walker, J.R. / Yermekbayeva, L. / Seitova, A. / Kania, J. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionSep 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ephrin type-B receptor 3
B: Ephrin type-B receptor 3
C: Ephrin type-B receptor 3
B: CHLORIDE ION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5236
Polymers69,2963
Non-polymers2283
Water4,252236
1
A: Ephrin type-B receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1952
Polymers23,0991
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ephrin type-B receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2303
Polymers23,0991
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ephrin type-B receptor 3


Theoretical massNumber of molelcules
Total (without water)23,0991
Polymers23,0991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.160, 102.160, 117.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Ephrin type-B receptor 3 / EPH-like kinase 2 / EK2 / hEK2 / Tyrosine-protein kinase TYRO6


Mass: 23098.617 Da / Num. of mol.: 3 / Fragment: Ligand binding domain (UNP residues 39-211)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHB3, ETK2, HEK2, TYR06, TYRO6 / Plasmid: PFHMSP-LIC-C / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: P54753, receptor protein-tyrosine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 291.1 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6 M AMMONIUM SULFATE, 5% ISOPROPANOL, 0.1 M BIS-TRIS,PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.1K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97895 / Wavelength: 0.97895 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 21, 2010
RadiationMonochromator: DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 37051 / Num. obs: 37051 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Rsym value: 0.154 / Net I/σ(I): 20.048
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 3.04 / Rsym value: 0.765 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ETP

3etp


Resolution: 2.1→19.75 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.157 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23462 1835 5 %RANDOM
Rwork0.18445 ---
obs0.18695 34833 99.14 %-
all-37051 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.008 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4014 0 11 236 4261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224137
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9265630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5735496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67823.55200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70615642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7671528
X-RAY DIFFRACTIONr_chiral_restr0.0970.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213206
X-RAY DIFFRACTIONr_mcbond_it0.8441.52506
X-RAY DIFFRACTIONr_mcangle_it1.56424049
X-RAY DIFFRACTIONr_scbond_it2.24531631
X-RAY DIFFRACTIONr_scangle_it3.534.51581
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 149 -
Rwork0.184 2483 -
obs--99.28 %
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)
11.59990.57380.15311.5323-0.08031.4167-0.01150.0175-0.0487-0.04030.00480.04330.06960.02720.00680.0282-0.0179-0.01460.01760.00680.023847.516816.52398.291
21.52940.40970.12391.2896-0.22231.80390.1084-0.10460.00240.1163-0.1286-0.134-0.13230.22160.02010.0422-0.0402-0.01530.06450.03540.04458.754149.9689-13.6906
32.0365-0.3432-0.04371.6449-0.42021.2946-0.0210.16880.082-0.0372-0.00880.0043-0.0143-0.00120.02990.00570.00130.00620.04070.01490.022279.429925.13164.2033
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999

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