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- PDB-3zfy: Crystal structure of EphB3 -

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Basic information

Entry
Database: PDB / ID: 3zfy
TitleCrystal structure of EphB3
ComponentsEPHRIN TYPE-B RECEPTOR 3
KeywordsTRANSFERASE
Function / homology
Function and homology information


urogenital system development / ephrin receptor activity / axon guidance receptor activity / central nervous system projection neuron axonogenesis / regulation of cell-cell adhesion / dendritic spine development / corpus callosum development / transmembrane-ephrin receptor activity / dendritic spine morphogenesis / retinal ganglion cell axon guidance ...urogenital system development / ephrin receptor activity / axon guidance receptor activity / central nervous system projection neuron axonogenesis / regulation of cell-cell adhesion / dendritic spine development / corpus callosum development / transmembrane-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) / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ephrin type-B receptor 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDebreczeni, J.E. / Overman, R. / Truman, C. / McAlister, M. / Attwood, T.K.
CitationJournal: Protein Sci. / Year: 2014
Title: Completing the Structural Family Portrait of the Human Ephb Tyrosine Kinase Domains
Authors: Overman, R.C. / Debreczeni, J.E. / Truman, C.M. / Mcalister, M.S. / Attwood, T.K.
History
DepositionDec 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Apr 9, 2014Group: Database references
Revision 1.3May 7, 2014Group: Database references
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)67,5312
Polymers67,5312
Non-polymers00
Water2,306128
1
A: EPHRIN TYPE-B RECEPTOR 3


Theoretical massNumber of molelcules
Total (without water)33,7661
Polymers33,7661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EPHRIN TYPE-B RECEPTOR 3


Theoretical massNumber of molelcules
Total (without water)33,7661
Polymers33,7661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.990, 56.488, 61.354
Angle α, β, γ (deg.)93.02, 90.65, 90.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein EPHRIN TYPE-B RECEPTOR 3 / EPH-LIKE TYROSINE KINASE 2 / EPH-LIKE KINASE 2 / EMBRYONIC KINASE 2 / EK2 / HEK2 / TYROSINE-PROTEIN ...EPH-LIKE TYROSINE KINASE 2 / EPH-LIKE KINASE 2 / EMBRYONIC KINASE 2 / EK2 / HEK2 / TYROSINE-PROTEIN KINASE TYRO6 / EPHB3


Mass: 33765.711 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 616-910
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
References: UniProt: P54753, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→61.2 Å / Num. obs: 29560 / % possible obs: 92.1 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.68
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 3.83 / % possible all: 83

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→61.26 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.901 / SU B: 13.171 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25188 1515 5.1 %RANDOM
Rwork0.22406 ---
obs0.22552 28046 92.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.017 Å2
Baniso -1Baniso -2Baniso -3
1--2.78 Å20.18 Å20.09 Å2
2---1.99 Å2-0.18 Å2
3---4.75 Å2
Refinement stepCycle: LAST / Resolution: 2.2→61.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3970 0 0 128 4098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194070
X-RAY DIFFRACTIONr_bond_other_d0.0020.022701
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.9595532
X-RAY DIFFRACTIONr_angle_other_deg0.93436571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8945508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62323.736174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35315658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1671528
X-RAY DIFFRACTIONr_chiral_restr0.0680.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214500
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02832
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 93 -
Rwork0.286 1679 -
obs--74.67 %
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)
13.023-0.2783-0.05943.62-0.01891.0506-0.0834-0.60240.22170.69950.1168-0.0178-0.08260.0722-0.03340.1430.0273-0.00790.1461-0.03690.058410.1726-1.542-0.1587
23.74130.45880.00613.95650.47931.2514-0.14630.72430.2697-0.72110.1430.0275-0.1512-0.0920.00330.1368-0.0299-0.00670.15980.06330.031931.7141-29.9917-23.2166
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A595 - 892
2X-RAY DIFFRACTION2B595 - 892

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