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- PDB-3zfm: Crystal structure of EphB2 -

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Basic information

Entry
Database: PDB / ID: 3zfm
TitleCrystal structure of EphB2
ComponentsEPHRIN TYPE-B RECEPTOR 2
KeywordsTRANSFERASE
Function / homology
Function and homology information


regulation of T-helper 17 type immune response / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / negative regulation of NMDA glutamate receptor activity / hindbrain tangential cell migration / L1CAM interactions / vesicle-mediated intercellular transport / positive regulation of NMDA glutamate receptor activity / regulation of body fluid levels / urogenital system development / optic nerve morphogenesis ...regulation of T-helper 17 type immune response / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / negative regulation of NMDA glutamate receptor activity / hindbrain tangential cell migration / L1CAM interactions / vesicle-mediated intercellular transport / positive regulation of NMDA glutamate receptor activity / regulation of body fluid levels / urogenital system development / optic nerve morphogenesis / tight junction assembly / postsynaptic membrane assembly / neuron projection retraction / axon guidance receptor activity / central nervous system projection neuron axonogenesis / negative regulation of axonogenesis / positive regulation of long-term neuronal synaptic plasticity / regulation of autophagosome assembly / positive regulation of dendritic spine morphogenesis / dendritic spine development / corpus callosum development / positive regulation of synaptic plasticity / camera-type eye morphogenesis / regulation of filopodium assembly / regulation of behavioral fear response / transmembrane-ephrin receptor activity / positive regulation of protein localization to cell surface / commissural neuron axon guidance / dendritic spine morphogenesis / negative regulation of cell adhesion / negative regulation of Ras protein signal transduction / retinal ganglion cell axon guidance / axonal fasciculation / positive regulation of synapse assembly / EPH-Ephrin signaling / regulation of receptor signaling pathway via JAK-STAT / Ephrin signaling / positive regulation of immunoglobulin production / inner ear morphogenesis / B cell activation / roof of mouth development / regulation of neuronal synaptic plasticity / regulation of blood coagulation / EPH-ephrin mediated repulsion of cells / negative regulation of cytokine production involved in inflammatory response / ephrin receptor signaling pathway / positive regulation of B cell proliferation / EPHB-mediated forward signaling / hippocampal mossy fiber to CA3 synapse / negative regulation of protein phosphorylation / learning / positive regulation of long-term synaptic potentiation / positive regulation of protein localization to plasma membrane / axon guidance / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / positive regulation of tumor necrosis factor production / presynaptic membrane / nervous system development / amyloid-beta binding / postsynapse / postsynaptic membrane / protein tyrosine kinase activity / angiogenesis / cellular response to lipopolysaccharide / dendritic spine / learning or memory / positive regulation of cell migration / phosphorylation / axon / signaling receptor binding / neuronal cell body / glutamatergic synapse / dendrite / protein-containing complex binding / positive regulation of gene expression / cell surface / extracellular region / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Ephrin type-B receptor 2, 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 2, 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 / Growth factor receptor cysteine-rich 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 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.27 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 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5May 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

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Assembly

Deposited unit
A: EPHRIN TYPE-B RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)33,6031
Polymers33,6031
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.590, 41.190, 54.470
Angle α, β, γ (deg.)92.65, 97.15, 114.79
Int Tables number1
Space group name H-MP1

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Components

#1: Protein EPHRIN TYPE-B RECEPTOR 2 / DEVELOPMENTALLY-REGULATED EPH-RELATED TYROSINE KINASE / ELK-RELATED TYROSINE KINASE / EPH TYROSINE ...DEVELOPMENTALLY-REGULATED EPH-RELATED TYROSINE KINASE / ELK-RELATED TYROSINE KINASE / EPH TYROSINE KINASE 3 / EPH-LIKE KINASE 5 / EK5 / HEK5 / RENAL CARCINOMA ANTIGEN NY-REN-47 / TYROSINE-PROTEIN KINASE TYRO5 / TYROSINE-PROTEIN KINASE RECEPTOR EPH-3 / EPHB2 / EPHHB2


Mass: 33603.387 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 604-898
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: P29323, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.99 Å3/Da / Density % sol: 38 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU SATURN / Detector: CCD / Date: Jul 29, 2009 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.27→37.17 Å / Num. obs: 45906 / % possible obs: 95.1 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 28.66 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.7
Reflection shellResolution: 2.27→2.39 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 10.3 / % possible all: 92.6

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→21.11 Å / Cor.coef. Fo:Fc: 0.843 / Cor.coef. Fo:Fc free: 0.8074 / SU R Cruickshank DPI: 0.404 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.387 / SU Rfree Blow DPI: 0.246 / SU Rfree Cruickshank DPI: 0.252
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2634 560 4.79 %RANDOM
Rwork0.2349 ---
obs0.2362 11689 94.1 %-
Displacement parametersBiso mean: 26.86 Å2
Baniso -1Baniso -2Baniso -3
1-1.7258 Å20.4573 Å2-0.4221 Å2
2--5.1799 Å20.9727 Å2
3----6.9057 Å2
Refine analyzeLuzzati coordinate error obs: 0.336 Å
Refinement stepCycle: LAST / Resolution: 2.27→21.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 0 83 2016
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011974HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.052679HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d669SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes49HARMONIC2
X-RAY DIFFRACTIONt_gen_planes284HARMONIC5
X-RAY DIFFRACTIONt_it1974HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.45
X-RAY DIFFRACTIONt_other_torsion18.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion265SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2354SEMIHARMONIC4
LS refinement shellResolution: 2.27→2.49 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2728 155 5.83 %
Rwork0.2737 2502 -
all0.2736 2657 -
obs--94.1 %

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