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- PDB-5zrx: Crystal Structure of EphA2/SHIP2 Complex -

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Basic information

Entry
Database: PDB / ID: 5zrx
TitleCrystal Structure of EphA2/SHIP2 Complex
ComponentsPhosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2,Ephrin type-A receptor 2
KeywordsPROTEIN BINDING / SAM DOMAIN / HETERODIMER / SIGNALING PROTEIN / CELL SIGNALING / RECEPTOR / TRANSMEMBRANE / TYROSINE-PROTEIN KINASE / CELL ADHESION
Function / homology
Function and homology information


notochord morphogenesis / EPH-Ephrin signaling / Synthesis of IP3 and IP4 in the cytosol / EPHA-mediated growth cone collapse / cellular lipid metabolic process / EPH-ephrin mediated repulsion of cells / inositol trisphosphate metabolic process / negative regulation of insulin-like growth factor receptor signaling pathway / Interleukin receptor SHC signaling / Synthesis of PIPs at the plasma membrane ...notochord morphogenesis / EPH-Ephrin signaling / Synthesis of IP3 and IP4 in the cytosol / EPHA-mediated growth cone collapse / cellular lipid metabolic process / EPH-ephrin mediated repulsion of cells / inositol trisphosphate metabolic process / negative regulation of insulin-like growth factor receptor signaling pathway / Interleukin receptor SHC signaling / Synthesis of PIPs at the plasma membrane / notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / axial mesoderm formation / inositol-polyphosphate 5-phosphatase activity / multicellular organism development / ruffle assembly / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration / leading edge membrane / negative regulation of chemokine production / phosphatidylinositol dephosphorylation / bone remodeling / transmembrane-ephrin receptor activity / endochondral ossification / post-anal tail morphogenesis / phosphatidylinositol biosynthetic process / response to growth factor / positive regulation of kinase activity / negative regulation of platelet-derived growth factor receptor signaling pathway / activation of GTPase activity / regulation of lamellipodium assembly / tight junction / branching involved in mammary gland duct morphogenesis / neural tube development / blood vessel morphogenesis / negative regulation of cytokine production / mammary gland epithelial cell proliferation / immune system process / negative regulation of DNA replication / blood vessel development / plasma membrane => GO:0005886 / phosphatidylinositol-3,4,5-trisphosphate binding / regulation of cell adhesion mediated by integrin / lamellipodium membrane / ephrin receptor signaling pathway / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / vasculogenesis / regulation of angiogenesis / keratinocyte differentiation / negative regulation of insulin receptor signaling pathway / SH2 domain binding / transmembrane receptor protein tyrosine kinase activity / cell chemotaxis / negative regulation of angiogenesis / osteoclast differentiation / regulation of ERK1 and ERK2 cascade / post-embryonic development / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of MAP kinase activity / filopodium / skeletal system development / protein localization to plasma membrane / cell motility / actin filament organization / positive regulation of protein localization to plasma membrane / cell surface receptor protein tyrosine kinase signaling pathway / axon guidance / response to insulin / neuron differentiation / receptor protein-tyrosine kinase / ruffle membrane / SH3 domain binding / endocytosis / osteoblast differentiation / glucose metabolic process / intrinsic apoptotic signaling pathway in response to DNA damage / cell migration / lamellipodium / negative regulation of neuron projection development / actin binding / cytoskeleton / receptor complex / cell adhesion / nuclear speck / defense response to Gram-positive bacterium / neuron projection / inflammatory response / negative regulation of cell population proliferation / negative regulation of gene expression / focal adhesion / Golgi apparatus / cell surface / ATP binding / nucleus
Similarity search - Function
Ephrin type-A receptor 2, ligand binding domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / 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-A receptor 2, ligand binding domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / 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 / Endonuclease/exonuclease/phosphatase / Putative ephrin-receptor like / Endonuclease/Exonuclease/phosphatase family / SAM domain (Sterile alpha motif) / Endonuclease/exonuclease/phosphatase superfamily / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / 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 / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain 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 / 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
Similarity search - Domain/homology
Ephrin type-A receptor 2 / Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWang, Y. / Shang, Y. / Li, J. / Chen, W. / Li, G. / Wan, J. / Liu, W. / Zhang, M.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0501903 China
CitationJournal: Elife / Year: 2018
Title: Specific Eph receptor-cytoplasmic effector signaling mediated by SAM-SAM domain interactions.
Authors: Wang, Y. / Shang, Y. / Li, J. / Chen, W. / Li, G. / Wan, J. / Liu, W. / Zhang, M.
History
DepositionApr 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2,Ephrin type-A receptor 2
B: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2,Ephrin type-A receptor 2


Theoretical massNumber of molelcules
Total (without water)35,2432
Polymers35,2432
Non-polymers00
Water4,918273
1
A: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2,Ephrin type-A receptor 2


Theoretical massNumber of molelcules
Total (without water)17,6221
Polymers17,6221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2,Ephrin type-A receptor 2


Theoretical massNumber of molelcules
Total (without water)17,6221
Polymers17,6221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.283, 43.344, 46.377
Angle α, β, γ (deg.)90.000, 95.350, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1481-

HOH

DetailsThe biological assembly is heterodimer of two SAM domains. However, two domains were expressed as a fused single chain protein in this structure.

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Components

#1: Protein Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2,Ephrin type-A receptor 2 / AblSH3-binding protein / Inositol polyphosphate phosphatase-like protein 1 / INPPL-1 / SH2 domain- ...AblSH3-binding protein / Inositol polyphosphate phosphatase-like protein 1 / INPPL-1 / SH2 domain-containing inositol 5'-phosphatase 2 / SHIP-2 / Epithelial cell kinase / Tyrosine-protein kinase receptor ECK / Tyrosine-protein kinase receptor MPK-5 / Tyrosine-protein kinase receptor SEK-2


Mass: 17621.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fusion protein of SAM domain from Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 and Ephrin type-A receptor 2
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Inppl1, Ship2, Epha2, Eck, Myk2, Sek2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6P549, UniProt: Q03145, phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / 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 Å3/Da / Density % sol: 38.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7
Details: 0.2M Succinic acid pH 7.0, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 43485 / % possible obs: 99 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.029 / Rrim(I) all: 0.056 / Χ2: 1.951 / Net I/σ(I): 14.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.533.50.62421310.870.3860.7361.35598.1
1.53-1.553.60.55821820.8740.3410.6561.31799.8
1.55-1.583.60.4521630.9080.2750.5281.38299.9
1.58-1.623.60.37821850.9450.2310.4441.423100
1.62-1.653.60.31321870.9640.1910.3671.50399.8
1.65-1.693.60.27421570.9640.1680.3221.497100
1.69-1.733.60.23722050.970.1450.2781.52299.8
1.73-1.783.70.18621700.9820.1130.2181.61499.9
1.78-1.833.70.14721880.990.0890.1721.62100
1.83-1.893.60.12921810.9910.0790.1521.857100
1.89-1.963.70.09921890.9930.060.1161.869100
1.96-2.043.70.08121920.9940.0490.0952.086100
2.04-2.133.70.06622000.9960.040.0782.18299.8
2.13-2.243.70.05721800.9960.0350.0672.30299.9
2.24-2.383.60.05121920.9970.0310.062.48299.8
2.38-2.563.60.04922270.9970.030.0582.85399.8
2.56-2.823.50.04621580.9970.0290.0543.05499.5
2.82-3.233.50.04422120.9970.0270.0523.14799.8
3.23-4.073.50.03221770.9970.020.0382.15797.1
4.07-503.40.03120090.9980.020.0371.87487.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KKA and 2K4P

3kka

2k4p


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.928 / SU ML: 0.047 / SU R Cruickshank DPI: 0.0741 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.069
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1911 2188 5 %RANDOM
Rwork0.1434 ---
obs0.1458 41294 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 85.36 Å2 / Biso mean: 31.151 Å2 / Biso min: 15.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-0.66 Å2
2--0.7 Å20 Å2
3----0.74 Å2
Refinement stepCycle: final / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 0 273 2280
Biso mean---45.77 -
Num. residues----251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192090
X-RAY DIFFRACTIONr_bond_other_d0.0020.021949
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.9592828
X-RAY DIFFRACTIONr_angle_other_deg0.95334515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5495260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.19724.476105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45615382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7471514
X-RAY DIFFRACTIONr_chiral_restr0.0760.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022324
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02430
X-RAY DIFFRACTIONr_rigid_bond_restr1.39534039
X-RAY DIFFRACTIONr_sphericity_free29.5895162
X-RAY DIFFRACTIONr_sphericity_bonded13.13354106
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 178 -
Rwork0.253 2921 -
all-3099 -
obs--96.33 %
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)
10.01140.0097-0.05190.0094-0.04190.25710.0001-0.00150.0021-0.0007-0.00860.0031-0.0320.00020.00840.02930.0039-0.02290.0335-0.00160.019-11.023416.701435.5416
20.10680.0617-0.02620.3133-0.14720.073-0.0078-0.00660.0161-0.01990.01850.01990.01020.0025-0.01070.0165-0.0006-0.01770.037-0.00280.0198-14.379725.820811.6803
30.1343-0.11520.10490.1082-0.08760.08310.0131-0.0245-0.0192-0.00270.00250.00810.0107-0.0264-0.01560.0256-0.0059-0.02350.05090.00650.0219-24.67545.415920.3555
40.1843-0.12830.12940.2129-0.07950.0937-0.0168-0.00680.0087-0.0079-0.0005-0.0019-0.0222-0.00750.01720.02660.0011-0.02570.0287-0.00020.0288-33.377425.2753-1.15
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A906 - 970
2X-RAY DIFFRACTION2B907 - 969
3X-RAY DIFFRACTION3A1196 - 1256
4X-RAY DIFFRACTION4B1196 - 1257

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