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- PDB-1b0x: THE CRYSTAL STRUCTURE OF AN EPH RECEPTOR SAM DOMAIN REVEALS A MEC... -

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Basic information

Entry
Database: PDB / ID: 1b0x
TitleTHE CRYSTAL STRUCTURE OF AN EPH RECEPTOR SAM DOMAIN REVEALS A MECHANISM FOR MODULAR DIMERIZATION.
ComponentsPROTEIN (EPHA4 RECEPTOR TYROSINE KINASE)
KeywordsTRANSFERASE / RECEPTOR TYROSINE KINASE / PROTEIN INTERACTION MODULE / DIMERIZATION DOMAIN
Function / homology
Function and homology information


EPH-Ephrin signaling / DH domain binding / neuron projection fasciculation / : / EPHA-mediated growth cone collapse / negative regulation of proteolysis involved in protein catabolic process / corticospinal tract morphogenesis / EPH-ephrin mediated repulsion of cells / regulation of astrocyte differentiation / neuron projection guidance ...EPH-Ephrin signaling / DH domain binding / neuron projection fasciculation / : / EPHA-mediated growth cone collapse / negative regulation of proteolysis involved in protein catabolic process / corticospinal tract morphogenesis / EPH-ephrin mediated repulsion of cells / regulation of astrocyte differentiation / neuron projection guidance / nephric duct morphogenesis / fasciculation of sensory neuron axon / fasciculation of motor neuron axon / synapse pruning / negative regulation of cellular response to hypoxia / negative regulation of axon regeneration / transmembrane-ephrin receptor activity / glial cell migration / PH domain binding / regulation of modification of synaptic structure / GPI-linked ephrin receptor activity / regulation of synapse pruning / adherens junction organization / positive regulation of dendrite morphogenesis / regulation of dendritic spine morphogenesis / negative regulation of cell adhesion / motor neuron axon guidance / innervation / adult walking behavior / regulation of GTPase activity / negative regulation of epithelial to mesenchymal transition / regulation of axonogenesis / positive regulation of amyloid-beta formation / positive regulation of intracellular signal transduction / negative regulation of long-term synaptic potentiation / cochlea development / ephrin receptor signaling pathway / axonal growth cone / ephrin receptor binding / axon terminus / transmembrane receptor protein tyrosine kinase activity / positive regulation of cell adhesion / axon guidance / protein tyrosine kinase binding / peptidyl-tyrosine phosphorylation / negative regulation of cell migration / dendritic shaft / positive regulation of JNK cascade / adherens junction / filopodium / neuromuscular junction / receptor protein-tyrosine kinase / postsynaptic density membrane / negative regulation of ERK1 and ERK2 cascade / Schaffer collateral - CA1 synapse / cellular response to amyloid-beta / negative regulation of neuron projection development / protein autophosphorylation / presynaptic membrane / early endosome membrane / perikaryon / dendritic spine / negative regulation of neuron apoptotic process / postsynaptic membrane / mitochondrial outer membrane / protein kinase activity / cell adhesion / protein stabilization / positive regulation of cell migration / axon / positive regulation of cell population proliferation / dendrite / glutamatergic synapse / cell surface / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Ephrin type-A receptor 4, SAM domain / Ephrin type-A receptor 4, 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 type-A receptor 4, SAM domain / Ephrin type-A receptor 4, 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 / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/Threonine protein kinases, 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-A receptor 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2 Å
AuthorsStapleton, D. / Balan, I. / Pawson, T. / Sicheri, F.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: The crystal structure of an Eph receptor SAM domain reveals a mechanism for modular dimerization.
Authors: Stapleton, D. / Balan, I. / Pawson, T. / Sicheri, F.
History
DepositionNov 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0May 3, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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: PROTEIN (EPHA4 RECEPTOR TYROSINE KINASE)


Theoretical massNumber of molelcules
Total (without water)10,2651
Polymers10,2651
Non-polymers00
Water95553
1
A: PROTEIN (EPHA4 RECEPTOR TYROSINE KINASE)

A: PROTEIN (EPHA4 RECEPTOR TYROSINE KINASE)


Theoretical massNumber of molelcules
Total (without water)20,5312
Polymers20,5312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)77.140, 77.140, 24.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein PROTEIN (EPHA4 RECEPTOR TYROSINE KINASE)


Mass: 10265.485 Da / Num. of mol.: 1 / Fragment: SAM DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BL21 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: Q03137
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.66 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mg/mlprotein1drop
27 mMHEPES1drop
3100 mMcacodylate1reservoir
47 %(w/v)PEG80001reservoir
520 %(v/v)ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Details: OSMIC MULTILAYER OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 17787 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.04
Reflection
*PLUS
Num. obs: 5663 / Observed criterion σ(I): -3 / Num. measured all: 17787 / Rmerge(I) obs: 0.004

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Processing

Software
NameVersionClassification
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.278 -5 %RANDOM
Rwork0.229 ---
obs-5498 94.6 %-
Displacement parametersBiso mean: 22.3 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms695 0 0 53 748
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.38
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.01

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