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- PDB-4et7: Crystal structure of Eph receptor 5 -

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Basic information

Entry
Database: PDB / ID: 4et7
TitleCrystal structure of Eph receptor 5
ComponentsEphrin type-A receptor 5
KeywordsTRANSFERASE / eph receptor / ATP-binding / Glycoprotein / Nucleotide-binding / Phosphoprotein / Transmembrane / Tyrosine-protein kinase
Function / homology
Function and homology information


positive regulation of CREB transcription factor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / regulation of insulin secretion involved in cellular response to glucose stimulus / ephrin receptor activity / EPH-Ephrin signaling / regulation of GTPase activity / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway ...positive regulation of CREB transcription factor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / regulation of insulin secretion involved in cellular response to glucose stimulus / ephrin receptor activity / EPH-Ephrin signaling / regulation of GTPase activity / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / neuron development / rough endoplasmic reticulum / cAMP-mediated signaling / axon guidance / hippocampus development / regulation of actin cytoskeleton organization / receptor protein-tyrosine kinase / axon / external side of plasma membrane / neuronal cell body / dendrite / perinuclear region of cytoplasm / ATP binding / plasma membrane
Similarity search - Function
Ephrin type-A receptor 5, ligand binding 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. ...Ephrin type-A receptor 5, ligand binding 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) / Galactose-binding domain-like / 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 / 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 / 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 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsShi, J.H. / Zhu, W.L. / Song, J.X.
CitationJournal: To be Published
Title: Crystal structure of Eph receptor 5
Authors: Shi, J.H. / Zhu, W.L. / Song, J.X.
History
DepositionApr 24, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ephrin type-A receptor 5


Theoretical massNumber of molelcules
Total (without water)20,3211
Polymers20,3211
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.040, 82.721, 81.166
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 5 / Brain-specific kinase / EPH homology kinase 1 / EHK-1 / EPH-like kinase 7 / EK7 / hEK7


Mass: 20320.748 Da / Num. of mol.: 1 / Fragment: UNP residues 59-235 / Mutation: C233A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BSK, EHK1, EPHA5, HEK7, TYRO4 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami (DE3)
References: UniProt: P54756, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE PROTEIN SEQUENCE IS DERIVED FROM THE EPHA5 ISOFORM B (NP_872272) WHICH HAS GLU AT POSITION 232.

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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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M ammonium sulfate, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jun 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→41.361 Å / Num. all: 5833 / Num. obs: 5385 / % possible obs: 99.98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 23.12 % / Rsym value: 0.134 / Net I/σ(I): 1.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
PROTEUM PLUSPLUSdata collection
SAINTdata reduction
PROTEUM PLUSPLUSdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CKH

3ckh


Resolution: 2.6→20.68 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 28.21 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE INCLUDES THE REFLECTIONS UNTIL 2.08 A BUT AUTHOR DID NOT USE THE DATA FOR RESOLUTION 2.6-2.08A, THAT IS NOT GOOD FOR REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2824 538 9.99 %RANDOM
Rwork0.2049 ---
all0.2194 5559 --
obs0.212 5385 90.63 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.606 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso max: 139.26 Å2 / Biso mean: 31.347 Å2 / Biso min: 9.38 Å2
Baniso -1Baniso -2Baniso -3
1--5.191 Å20 Å2-0 Å2
2--15.266 Å20 Å2
3----10.075 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1399 0 0 36 1435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071429
X-RAY DIFFRACTIONf_angle_d1.1411931
X-RAY DIFFRACTIONf_chiral_restr0.081208
X-RAY DIFFRACTIONf_plane_restr0.003252
X-RAY DIFFRACTIONf_dihedral_angle_d19.319515
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.8610.3241240.2211085120983
2.861-3.2740.3341280.2221171129988
3.274-4.1190.2761370.21248138594
4.119-20.6810.2331490.1871343149297

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