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- PDB-1f0m: MONOMERIC STRUCTURE OF THE HUMAN EPHB2 SAM (STERILE ALPHA MOTIF) ... -

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Basic information

Entry
Database: PDB / ID: 1f0m
TitleMONOMERIC STRUCTURE OF THE HUMAN EPHB2 SAM (STERILE ALPHA MOTIF) DOMAIN
ComponentsEPHRIN TYPE-B RECEPTOR 2
KeywordsSIGNALING PROTEIN / SAM domain
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 / postsynaptic membrane assembly / urogenital system development / regulation of body fluid levels ...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 / postsynaptic membrane assembly / urogenital system development / regulation of body fluid levels / optic nerve morphogenesis / tight junction assembly / neuron projection retraction / axon guidance receptor activity / central nervous system projection neuron axonogenesis / negative regulation of axonogenesis / regulation of behavioral fear response / transmembrane-ephrin receptor activity / 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 / negative regulation of Ras protein signal transduction / positive regulation of protein localization to cell surface / commissural neuron axon guidance / dendritic spine morphogenesis / negative regulation of cell adhesion / 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 / inner ear morphogenesis / regulation of neuronal synaptic plasticity / B cell activation / roof of mouth development / regulation of blood coagulation / positive regulation of immunoglobulin production / 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 / axon guidance / positive regulation of protein localization to plasma membrane / 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 / amyloid-beta binding / nervous system development / postsynaptic membrane / postsynapse / angiogenesis / protein tyrosine kinase activity / cellular response to lipopolysaccharide / dendritic spine / learning or memory / positive regulation of cell migration / axon / phosphorylation / signaling receptor binding / dendrite / neuronal cell body / glutamatergic synapse / 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 / Resolution: 2.2 Å
AuthorsThanos, C.D. / Faham, S. / Goodwill, K.E. / Cascio, D. / Phillips, M. / Bowie, J.U.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Monomeric structure of the human EphB2 sterile alpha motif domain.
Authors: Thanos, C.D. / Faham, S. / Goodwill, K.E. / Cascio, D. / Phillips, M. / Bowie, J.U.
History
DepositionMay 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)9,4021
Polymers9,4021
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.837, 54.837, 65.545
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 2 / EPHB2


Mass: 9401.772 Da / Num. of mol.: 1 / Fragment: EPHB2 RECEPTOR FRAGMENT, SAM DOMAIN / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P29323
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% peg, 70 mM lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 25K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
250 mMHEPES1drop
387.5 mM1dropLi2SO4
415 %PEG60001drop
5100 mMHEPES1reservoir
6175 mM1reservoirLi2SO4
730 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1
DetectorType: OTHER / Detector: CCD / Date: Sep 8, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→500 Å / Num. all: 5449 / Num. obs: 4963 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 31
Reflection shellResolution: 2.2→50 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.048 / Num. unique all: 5273 / % possible all: 91.1
Reflection shell
*PLUS
% possible obs: 91.1 % / Rmerge(I) obs: 0.302

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.264 524 random
Rwork0.243 --
all0.243 5449 -
obs0.243 4963 -
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms566 0 0 113 679
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg2.097
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg

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