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- PDB-8j1i: Crystal Structure of EphA8/SASH1 Complex -

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Basic information

Entry
Database: PDB / ID: 8j1i
TitleCrystal Structure of EphA8/SASH1 Complex
Components
  • Ephrin type-A receptor 8
  • SAM and SH3 domain-containing protein 1
KeywordsSIGNALING PROTEIN / Complex / SAM-SAM / EphA8 receptor / SASH1
Function / homology
Function and homology information


regulation of protein K63-linked ubiquitination / regulation of protein autoubiquitination / EPH-Ephrin signaling / EPHA-mediated growth cone collapse / substrate-dependent cell migration / EPH-ephrin mediated repulsion of cells / ephrin receptor activity / regulation of epithelial cell migration / GPI-linked ephrin receptor activity / cellular response to follicle-stimulating hormone stimulus ...regulation of protein K63-linked ubiquitination / regulation of protein autoubiquitination / EPH-Ephrin signaling / EPHA-mediated growth cone collapse / substrate-dependent cell migration / EPH-ephrin mediated repulsion of cells / ephrin receptor activity / regulation of epithelial cell migration / GPI-linked ephrin receptor activity / cellular response to follicle-stimulating hormone stimulus / positive regulation of lipopolysaccharide-mediated signaling pathway / transmembrane-ephrin receptor activity / mitogen-activated protein kinase kinase kinase binding / positive regulation of p38MAPK cascade / neuron remodeling / growth factor binding / regulation of cell adhesion mediated by integrin / G-protein alpha-subunit binding / ephrin receptor signaling pathway / regulation of cell adhesion / positive regulation of endothelial cell migration / axon guidance / receptor protein-tyrosine kinase / positive regulation of non-canonical NF-kappaB signal transduction / protein polyubiquitination / positive regulation of angiogenesis / neuron projection development / early endosome membrane / positive regulation of MAPK cascade / protein autophosphorylation / molecular adaptor activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / neuron projection / dendrite / protein kinase binding / protein-containing complex / nucleoplasm / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Ephrin type-A receptor 8, ligand binding domain / SAM and SH3 domain-containing protein 1, SH3 domain / SASH1, SAM domain repeat 1 / SASH1, SAM domain repeat 2 / SAM/SH3 domain-containing / SLy Proteins Associated Disordered Region / 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 8, ligand binding domain / SAM and SH3 domain-containing protein 1, SH3 domain / SASH1, SAM domain repeat 1 / SASH1, SAM domain repeat 2 / SAM/SH3 domain-containing / SLy Proteins Associated Disordered Region / 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 / Variant SH3 domain / SAM domain (Sterile alpha motif) / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed 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 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 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 8 / SAM and SH3 domain-containing protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLiu, W. / Li, J. / Ding, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of EphA8 and SASH1 complex at 1.60 Angstroms resolution
Authors: Liu, W. / Li, J. / Ding, Y.
History
DepositionApr 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
8: Ephrin type-A receptor 8
H: SAM and SH3 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)15,9872
Polymers15,9872
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.937, 84.576, 97.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Ephrin type-A receptor 8 / EPH- and ELK-related kinase / Tyrosine-protein kinase receptor EEK


Mass: 7489.671 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Epha8, Eek / Production host: Escherichia coli (E. coli)
References: UniProt: O09127, receptor protein-tyrosine kinase
#2: Protein SAM and SH3 domain-containing protein 1


Mass: 8497.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sash1 / Production host: Escherichia coli (E. coli) / References: UniProt: P59808
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 3.12 Å3/Da / Density % sol: 60.55 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: PEG 1500,10% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 25509 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.014 / Rrim(I) all: 0.049 / Χ2: 0.607 / Net I/σ(I): 5.9 / Num. measured all: 332592
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.6-1.6313.41.21212420.7770.9350.341.2590.433100
1.63-1.6613.40.91112650.890.970.2550.9460.439100
1.66-1.6913.30.75412420.9150.9770.2120.7840.438100
1.69-1.7213.20.58212620.9460.9860.1650.6050.477100
1.72-1.76130.49112760.9550.9880.140.5110.462100
1.76-1.812.30.38812380.9650.9910.1150.4050.515100
1.8-1.8512.60.31212700.9780.9940.0910.3250.568100
1.85-1.913.60.36112410.980.9950.1010.3750.623100
1.9-1.9513.40.27112740.9760.9940.0770.2821.024100
1.95-2.0213.30.14412680.9950.9990.0410.150.53100
2.02-2.09130.12812760.9970.9990.0370.1330.676100
2.09-2.1712.30.09112580.9970.9990.0270.0950.586100
2.17-2.2712.90.11112840.9960.9990.0320.1151.098100
2.27-2.3913.60.07112600.99810.020.0740.621100
2.39-2.5413.40.05712890.99910.0160.0590.587100
2.54-2.7412.90.04912670.99910.0140.0510.594100
2.74-3.0112.80.04212980.99910.0120.0440.579100
3.01-3.4513.50.03612890.99910.010.0380.59100
3.45-4.3412.40.03213210.99910.0090.0330.656100
4.34-5012.40.03613890.99910.0110.0380.62899.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.19.2-4158refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FXF

6fxf


Resolution: 1.6→32.01 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.633 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2368 1248 4.9 %RANDOM
Rwork0.19704 ---
obs0.19882 24220 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.117 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2---0.44 Å20 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.6→32.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 0 127 1169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131083
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151029
X-RAY DIFFRACTIONr_angle_refined_deg2.1781.6361465
X-RAY DIFFRACTIONr_angle_other_deg1.6391.5842368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3335137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79922.54259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88315197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.049158
X-RAY DIFFRACTIONr_chiral_restr0.1130.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021233
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02239
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3462.738545
X-RAY DIFFRACTIONr_mcbond_other2.3392.729544
X-RAY DIFFRACTIONr_mcangle_it3.5514.067683
X-RAY DIFFRACTIONr_mcangle_other3.5524.078684
X-RAY DIFFRACTIONr_scbond_it3.5432.976538
X-RAY DIFFRACTIONr_scbond_other3.542.985539
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0894.356782
X-RAY DIFFRACTIONr_long_range_B_refined7.4934.3541270
X-RAY DIFFRACTIONr_long_range_B_other7.32133.4151235
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.601→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 92 -
Rwork0.279 1735 -
obs--98.76 %
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)
10.9887-1.80580.80334.2812-0.55851.5158-0.1934-0.0935-0.2020.50550.38220.3583-0.04980.0946-0.18880.08620.07110.0560.07210.03420.0603-7.40625.135114.5096
22.34091.9427-0.23921.6885-0.38440.4821-0.11050.0312-0.022-0.09480.0224-0.05880.01620.01230.08810.00820.00220.01570.06350.01490.08032.489217.0856-1.7371
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION18931 - 996
2X-RAY DIFFRACTION2H624 - 690

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