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- PDB-1b4f: OLIGOMERIC STRUCTURE OF THE HUMAN EPHB2 RECEPTOR SAM DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1b4f
TitleOLIGOMERIC STRUCTURE OF THE HUMAN EPHB2 RECEPTOR SAM DOMAIN
ComponentsEPHB2
KeywordsSIGNAL TRANSDUCTION / SAM DOMAIN / EPH RECEPTOR / OLIGOMER
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 / positive regulation of synaptic plasticity / corpus callosum development / regulation of filopodium assembly / camera-type eye morphogenesis / regulation of behavioral fear response / transmembrane-ephrin receptor activity / commissural neuron axon guidance / positive regulation of protein localization to cell surface / negative regulation of cell adhesion / dendritic spine morphogenesis / negative regulation of Ras protein signal transduction / axonal fasciculation / positive regulation of synapse assembly / regulation of receptor signaling pathway via JAK-STAT / EPH-Ephrin signaling / Ephrin signaling / positive regulation of immunoglobulin production / inner ear morphogenesis / retinal ganglion cell axon guidance / 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 / receptor protein-tyrosine kinase / negative regulation of ERK1 and ERK2 cascade / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / positive regulation of tumor necrosis factor production / presynaptic membrane / nervous system development / amyloid-beta binding / postsynapse / cellular response to lipopolysaccharide / postsynaptic membrane / protein tyrosine kinase activity / angiogenesis / 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 / Transcription Factor, Ets-1 / 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-B receptor 2, ligand binding domain / Transcription Factor, Ets-1 / 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 / DNA polymerase; domain 1 / 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ephrin type-B receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsThanos, C.D. / Goodwill, K.E. / Bowie, J.U.
CitationJournal: Science / Year: 1999
Title: Oligomeric structure of the human EphB2 receptor SAM domain.
Authors: Thanos, C.D. / Goodwill, K.E. / Bowie, J.U.
History
DepositionDec 20, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 11, 2019Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: EPHB2
B: EPHB2
C: EPHB2
D: EPHB2
E: EPHB2
F: EPHB2
G: EPHB2
H: EPHB2


Theoretical massNumber of molelcules
Total (without water)75,2148
Polymers75,2148
Non-polymers00
Water12,340685
1
A: EPHB2
B: EPHB2

C: EPHB2

D: EPHB2


Theoretical massNumber of molelcules
Total (without water)37,6074
Polymers37,6074
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_574y,-x+2,z-1/41
crystal symmetry operation4_564y,-x+1,z-1/41
2
E: EPHB2
F: EPHB2

H: EPHB2

G: EPHB2


Theoretical massNumber of molelcules
Total (without water)37,6074
Polymers37,6074
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_574y,-x+2,z-1/41
crystal symmetry operation4_564y,-x+1,z-1/41
Unit cell
Length a, b, c (Å)73.897, 73.897, 104.547
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
EPHB2


Mass: 9401.772 Da / Num. of mol.: 8 / Fragment: SAM DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: VASCULAR / Cell: RENAL MICROVASCULAR ENDOTHELIAL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P29323
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 685 / 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: 1.96 Å3/Da / Density % sol: 37.2 %
Crystal growpH: 7 / Details: pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
2100 mMHEPES1reservoir
310 mMTris1reservoir
420 mMdithiothreitol1reservoir
530 mM1reservoirLi2SO4
626-30 %PEG10001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.96859, 0.97966, 0.97982, 1.0000
DetectorDate: Aug 1, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.968591
20.979661
30.979821
411
ReflectionResolution: 1.95→26 Å / Num. obs: 39547 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 16.9 Å2 / Rsym value: 0.047 / Net I/σ(I): 17.6
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 6.84 / Rsym value: 0.163 / % possible all: 98.7
Reflection
*PLUS
Num. measured all: 223269 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
Rmerge(I) obs: 0.163

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Processing

Software
NameVersionClassification
CNS0.4refinement
SHAKE-N-BAKEmodel building
DENZOdata reduction
SCALEPACKdata scaling
CNS0.4phasing
SHAKE-N-BAKEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→26 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 7659 10 %RANDOM
Rwork0.228 ---
obs0.228 76400 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.11 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.95→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4887 0 0 685 5572
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.028
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.18
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.731.5
X-RAY DIFFRACTIONc_mcangle_it3.672
X-RAY DIFFRACTIONc_scbond_it5.412
X-RAY DIFFRACTIONc_scangle_it6.92.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 1350 10.2 %
Rwork0.254 11924 -
obs--98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.18

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