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- PDB-3nru: Ligand binding domain of EPHA7 -

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Basic information

Entry
Database: PDB / ID: 3nru
TitleLigand binding domain of EPHA7
ComponentsEphrin receptor
KeywordsTRANSFERASE / KINASE
Function / homology
Function and homology information


: / regulation of protein autophosphorylation / regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of synapse assembly / nephric duct morphogenesis / negative regulation of collateral sprouting / axon guidance receptor activity / branching morphogenesis of a nerve / regulation of cell-cell adhesion / transmembrane-ephrin receptor activity ...: / regulation of protein autophosphorylation / regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of synapse assembly / nephric duct morphogenesis / negative regulation of collateral sprouting / axon guidance receptor activity / branching morphogenesis of a nerve / regulation of cell-cell adhesion / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / multicellular organism development / chemorepellent activity / positive regulation of kinase activity / retinal ganglion cell axon guidance / EPH-Ephrin signaling / regulation of postsynapse organization / negative chemotaxis / EPHA-mediated growth cone collapse / growth factor binding / plasma membrane => GO:0005886 / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / regulation of peptidyl-tyrosine phosphorylation / transmembrane receptor protein tyrosine kinase activity / ephrin receptor binding / regulation of ERK1 and ERK2 cascade / axon guidance / brain development / modulation of chemical synaptic transmission / neuromuscular junction / receptor protein-tyrosine kinase / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of neuron apoptotic process / protein tyrosine kinase activity / neuron apoptotic process / receptor complex / neuron projection / positive regulation of protein phosphorylation / phosphorylation / dendrite / neuronal cell body / glutamatergic synapse / apoptotic process / ATP binding / plasma membrane
Similarity search - Function
Ephrin type-A receptor 7, ligand binding domain / 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. ...Ephrin type-A receptor 7, ligand binding domain / 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) / Galactose-binding domain-like / 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 / 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 / Jelly Rolls / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ephrin type-A receptor 7 / Ephrin type-A receptor 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWalker, J.R. / Yermekbayeva, L. / Seitova, A. / Kania, J. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
CitationJournal: To be Published
Title: Ephrin A7 ligand binding domain
Authors: Walker, J.R. / Yermekbayeva, L. / Seitova, A. / Kania, J. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ephrin receptor
B: Ephrin receptor
C: Ephrin receptor
D: Ephrin receptor
E: Ephrin receptor
F: Ephrin receptor
G: Ephrin receptor
H: Ephrin receptor
I: Ephrin receptor
J: Ephrin receptor
K: Ephrin receptor
L: Ephrin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,78424
Polymers260,75312
Non-polymers1,03212
Water10,989610
1
A: Ephrin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8252
Polymers21,7291
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ephrin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0535
Polymers21,7291
Non-polymers3244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ephrin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8613
Polymers21,7291
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ephrin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9223
Polymers21,7291
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Ephrin receptor


Theoretical massNumber of molelcules
Total (without water)21,7291
Polymers21,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Ephrin receptor


Theoretical massNumber of molelcules
Total (without water)21,7291
Polymers21,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Ephrin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9223
Polymers21,7291
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Ephrin receptor


Theoretical massNumber of molelcules
Total (without water)21,7291
Polymers21,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Ephrin receptor


Theoretical massNumber of molelcules
Total (without water)21,7291
Polymers21,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Ephrin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8252
Polymers21,7291
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Ephrin receptor


Theoretical massNumber of molelcules
Total (without water)21,7291
Polymers21,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Ephrin receptor


Theoretical massNumber of molelcules
Total (without water)21,7291
Polymers21,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.617, 140.699, 143.783
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Ephrin receptor /


Mass: 21729.402 Da / Num. of mol.: 12 / Fragment: residues 29-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA7 / Plasmid: pFHMSP-LIC-C / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: B7ZLK0, UniProt: Q15375*PLUS, receptor protein-tyrosine kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 610 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 291 K / pH: 4.8
Details: 0.3 M NH4SO4, 0.6 M LiSO4, 0.1 M tri-NaCitrate pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 123900 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rsym value: 0.057 / Net I/σ(I): 36.4
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.555 / % possible all: 100

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WO1

2wo1


Resolution: 2.3→19.97 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.911 / SU B: 14.606 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26894 6230 5 %RANDOM
Rwork0.23505 ---
obs0.2368 117396 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.134 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2---0.19 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15203 0 52 610 15865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02215671
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9671.95621293
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05251877
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34324.927749
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.127152626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1181575
X-RAY DIFFRACTIONr_chiral_restr0.0640.22353
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02111819
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3481.59497
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.654215320
X-RAY DIFFRACTIONr_scbond_it0.79236174
X-RAY DIFFRACTIONr_scangle_it1.334.55973
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 448 -
Rwork0.285 8469 -
obs--99.27 %
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)
11.8024-0.4887-0.56162.8533-0.32112.4668-0.0245-0.03480.0694-0.180.0599-0.00470.10310.1411-0.03540.01810.01120.00840.095-0.02690.107912.1747-35.7298-9.4755
21.975-0.0136-0.6892.7301-0.0662.8155-0.0609-0.0565-0.02550.18540.03810.00030.1258-0.0720.02280.02210.01260.01930.10190.04280.1221-6.6514-36.92058.4968
32.70260.3833-0.15352.26150.3022.9080.1119-0.12080.08760.0419-0.06150.07280.05250.2382-0.05040.1469-0.052-0.06070.0604-0.0150.08649.4978-64.5202-33.5881
42.7003-0.60430.06863.092-0.893.6621-0.00220.00730.00380.15890.01710.0861-0.084-0.2428-0.0150.0556-0.0036-0.01870.07460.04730.048-9.3945-60.356639.4302
54.0585-0.08630.95612.48990.05381.97060.28160.20760.08170.1097-0.2766-0.0410.21030.1884-0.0050.03810.00460.00630.12730.00840.0293-34.4107-62.106512.5795
64.0984-1.09781.61892.4274-0.82264.36150.27450.395-0.2367-0.3779-0.20370.07910.28350.4738-0.07080.20440.1093-0.03530.0923-0.03030.1118.7231-12.9348-36.9913
72.55570.38280.02122.1674-0.57892.80580.114-0.03310.0245-0.1246-0.06130.11520.1246-0.0122-0.05270.02550.0199-0.03080.0634-0.02590.12440.589-58.5582-11.1787
82.580.73460.54452.78171.13333.19040.1253-0.3395-0.0710.5084-0.15610.04910.2357-0.29480.03080.1299-0.04310.01960.06950.00860.0167-5.2073-11.91134.6364
93.60750.221.07053.49921.22114.28760.47460.396-0.594-0.3457-0.0584-0.01650.54580.4335-0.41620.32360.2844-0.18380.291-0.18150.177-34.9326-78.824-6.5434
102.825-0.7897-1.36952.78861.45314.40530.0388-0.26730.13750.18240.1371-0.3671-0.16970.5993-0.1760.0547-0.0737-0.03670.179-0.0260.142829.8094-68.5176-59.3271
112.5456-0.23480.98053.8745-0.3584.9121-0.2264-0.05830.21130.15480.0402-0.0749-1.03630.0860.18620.4251-0.0096-0.04880.026-0.04880.118612.7852-40.9393-60.1722
123.8080.86530.35653.85720.2184.3612-0.51860.05850.5025-0.0370.43770.4182-0.6196-0.53750.08090.48160.1457-0.06190.16550.11050.2625-6.3038-38.9363-76.8974
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999
5X-RAY DIFFRACTION5E-10 - 9999
6X-RAY DIFFRACTION6F-10 - 9999
7X-RAY DIFFRACTION7G-10 - 9999
8X-RAY DIFFRACTION8H-10 - 9999
9X-RAY DIFFRACTION9I-10 - 9999
10X-RAY DIFFRACTION10J-10 - 9999
11X-RAY DIFFRACTION11K-10 - 9999
12X-RAY DIFFRACTION12L-10 - 9999

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