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- PDB-5zry: Crystal Structure of EphA6/Odin Complex -

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Basic information

Entry
Database: PDB / ID: 5zry
TitleCrystal Structure of EphA6/Odin Complex
ComponentsAnkyrin repeat and SAM domain-containing protein 1A,Ephrin type-A receptor 6
KeywordsPROTEIN BINDING / SAM DOMAIN / HETERODIMER / SIGNALING PROTEIN / CELL SIGNALING / RECEPTOR / TRANSMEMBRANE / TYROSINE-PROTEIN KINASE / CELL ADHESION
Function / homology
Function and homology information


regulation of ephrin receptor signaling pathway / EPH-Ephrin signaling / EPHA-mediated growth cone collapse / substrate-dependent cell migration / EPH-ephrin mediated repulsion of cells / multicellular organism development / transmembrane-ephrin receptor activity / positive regulation of kinase activity / neuron remodeling / plasma membrane => GO:0005886 ...regulation of ephrin receptor signaling pathway / EPH-Ephrin signaling / EPHA-mediated growth cone collapse / substrate-dependent cell migration / EPH-ephrin mediated repulsion of cells / multicellular organism development / transmembrane-ephrin receptor activity / positive regulation of kinase activity / neuron remodeling / plasma membrane => GO:0005886 / ephrin receptor signaling pathway / negative regulation of ubiquitin-dependent protein catabolic process / ephrin receptor binding / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / axon guidance / receptor protein-tyrosine kinase / receptor complex / neuron projection / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Ankyrin repeat and SAM domain-containing protein 1A / Ephrin type-A receptor 6, ligand binding domain / EPH-A6 , SAM domain / Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 1 / Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 2 / Domain of unknown function DUF3447 / Phosphotyrosine interaction domain (PTB/PID) / Tyrosine-protein kinase ephrin type A/B receptor-like / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain ...Ankyrin repeat and SAM domain-containing protein 1A / Ephrin type-A receptor 6, ligand binding domain / EPH-A6 , SAM domain / Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 1 / Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 2 / Domain of unknown function DUF3447 / Phosphotyrosine interaction domain (PTB/PID) / Tyrosine-protein kinase ephrin type A/B receptor-like / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / 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 (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 / Ankyrin repeats (3 copies) / Fibronectin type-III domain profile. / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / Galactose-binding-like domain superfamily / ankyrin repeats / Fibronectin type III / Fibronectin type III superfamily / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / 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
Ankyrin repeat and SAM domain-containing protein 1A / Ephrin type-A receptor 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsWang, Y. / Shang, Y. / Li, J. / Chen, W. / Li, G. / Wan, J. / Liu, W. / Zhang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Key R&D Program of China2016YFA0501903 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 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ankyrin repeat and SAM domain-containing protein 1A,Ephrin type-A receptor 6
B: Ankyrin repeat and SAM domain-containing protein 1A,Ephrin type-A receptor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,81911
Polymers43,7942
Non-polymers1,0259
Water6,900383
1
A: Ankyrin repeat and SAM domain-containing protein 1A,Ephrin type-A receptor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6117
Polymers21,8971
Non-polymers7156
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ankyrin repeat and SAM domain-containing protein 1A,Ephrin type-A receptor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2074
Polymers21,8971
Non-polymers3103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.985, 85.042, 98.383
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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

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Protein , 1 types, 2 molecules AB

#1: Protein Ankyrin repeat and SAM domain-containing protein 1A,Ephrin type-A receptor 6 / Odin / EPH homology kinase 2 / EHK-2


Mass: 21896.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Odin SAM1 - EphA6 SAM fusion protein / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Anks1a, Anks1, Kiaa0229, Odin, Epha6, Ehk-2, Ehk2 / Production host: Escherichia coli (E. coli)
References: UniProt: P59672, UniProt: Q62413, receptor protein-tyrosine kinase

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Non-polymers , 5 types, 392 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 1.86 Å3/Da / Density % sol: 33.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M HEPES sodium pH 7.5, 1.5M lithium sulfate monohydrate

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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: Jan 14, 2015
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: 1.3→50 Å / Num. obs: 79398 / % possible obs: 97.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.024 / Rrim(I) all: 0.059 / Χ2: 1.647 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.3-1.325.70.90337920.7850.390.9871.35495.1
1.32-1.355.70.83138170.8140.360.9091.39995
1.35-1.375.70.70738610.8640.3040.7721.38996.5
1.37-1.45.70.61538740.8820.2670.6721.36196.9
1.4-1.435.70.5439030.9150.2340.591.35297.3
1.43-1.465.70.42738960.930.1850.4671.39197.6
1.46-1.55.70.32339750.9660.140.3531.42898.4
1.5-1.545.80.26639610.9760.1150.2911.47998.8
1.54-1.595.80.22539790.9780.0970.2461.50398.7
1.59-1.645.80.239980.9810.0870.2191.71699.4
1.64-1.75.90.1740490.9860.0740.1861.61399.6
1.7-1.765.90.13639900.9920.0590.1481.64999.2
1.76-1.845.90.10140230.9950.0440.1111.68299.8
1.84-1.945.90.07940540.9960.0350.0871.71299.9
1.94-2.065.80.0639790.9970.0270.0661.81898.2
2.06-2.226.40.0540750.9980.0210.0541.871100
2.22-2.456.40.04540900.9980.0190.051.951100
2.45-2.86.50.0441130.9980.0170.0431.937100
2.8-3.536.30.03641670.9980.0150.0391.99299.6
3.53-505.40.03538020.9970.0170.0392.10887

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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, 2LMR

3kka

2lmr


Resolution: 1.3→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.304 / SU ML: 0.042 / SU R Cruickshank DPI: 0.0574 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.053
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1987 1947 2.5 %RANDOM
Rwork0.1695 ---
obs0.1703 77297 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 204.75 Å2 / Biso mean: 23.418 Å2 / Biso min: 12.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å2-0 Å2
2--0.53 Å20 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 1.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2607 0 60 383 3050
Biso mean--44.78 42.55 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192876
X-RAY DIFFRACTIONr_bond_other_d0.0020.022707
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9823913
X-RAY DIFFRACTIONr_angle_other_deg1.03836307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4315381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05623.435131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62115532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4121523
X-RAY DIFFRACTIONr_chiral_restr0.0980.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023188
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02603
X-RAY DIFFRACTIONr_rigid_bond_restr1.54435583
X-RAY DIFFRACTIONr_sphericity_free33.0085186
X-RAY DIFFRACTIONr_sphericity_bonded13.17655709
LS refinement shellResolution: 1.301→1.335 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 146 -
Rwork0.259 5441 -
all-5587 -
obs--94.3 %
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)
10.0198-0.0066-0.0080.37090.06910.07770.00590.00050.00090.0169-0.0070.0156-0.0257-0.01040.00110.07610.00170.00240.00150.00020.017639.56484.608105.867
20.09-0.09190.02920.32980.09890.08040.00310.00580.00220.0015-0.0011-0.0107-0.00170.0046-0.0020.0716-0.00640.00770.0014-0.00290.018444.47586.662131.043
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 195
2X-RAY DIFFRACTION2B35 - 195

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