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- PDB-3fy2: Human EphA3 Kinase and Juxtamembrane Region Bound to Substrate KQ... -

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Basic information

Entry
Database: PDB / ID: 3fy2
TitleHuman EphA3 Kinase and Juxtamembrane Region Bound to Substrate KQWDNYEFIW
Components
  • Ephrin type-A receptor 3
  • peptide substrate
KeywordsTRANSFERASE / receptor tyrosine kinase / juxtamembrane segment / structural genomics / peptide co-crystal structure / Structural Genomics Consortium / SGC / ATP-binding / Cell membrane / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Secreted / Transmembrane / Tyrosine-protein kinase
Function / homology
Function and homology information


fasciculation of sensory neuron axon / fasciculation of motor neuron axon / ephrin receptor activity / regulation of epithelial to mesenchymal transition / negative regulation of endocytosis / EPH-Ephrin signaling / regulation of GTPase activity / regulation of focal adhesion assembly / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells ...fasciculation of sensory neuron axon / fasciculation of motor neuron axon / ephrin receptor activity / regulation of epithelial to mesenchymal transition / negative regulation of endocytosis / EPH-Ephrin signaling / regulation of GTPase activity / regulation of focal adhesion assembly / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / cellular response to retinoic acid / regulation of microtubule cytoskeleton organization / axon guidance / positive regulation of protein localization to plasma membrane / regulation of actin cytoskeleton organization / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / positive regulation of neuron projection development / cell migration / actin cytoskeleton / nuclear membrane / early endosome / cell adhesion / dendrite / extracellular region / nucleoplasm / ATP binding / plasma membrane / cytosol
Similarity search - Function
Ephrin type-A receptor 3, 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 ...Ephrin type-A receptor 3, 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) / 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 / EGF-like domain signature 2. / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ephrin type-A receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsDavis, T. / Walker, J.R. / Mackenzie, F. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Febs J. / Year: 2009
Title: Structural recognition of an optimized substrate for the ephrin family of receptor tyrosine kinases.
Authors: Davis, T.L. / Walker, J.R. / Allali-Hassani, A. / Parker, S.A. / Turk, B.E. / Dhe-Paganon, S.
History
DepositionJan 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 3, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Revision 1.5Sep 6, 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

Downloads & links

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Assembly

Deposited unit
A: Ephrin type-A receptor 3
B: peptide substrate


Theoretical massNumber of molelcules
Total (without water)43,2492
Polymers43,2492
Non-polymers00
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-0.6 kcal/mol
Surface area14940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.824, 38.261, 76.365
Angle α, β, γ (deg.)90.000, 102.050, 90.000
Int Tables number4
Space group name H-MP1211
DetailsBIOLOGICAL UNIT IS THE SAME AS ASYMMETRIC UNIT

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Components

#1: Protein Ephrin type-A receptor 3 / Tyrosine-protein kinase receptor ETK1 / HEK / HEK4 / Tyrosine-protein kinase TYRO4


Mass: 41819.730 Da / Num. of mol.: 1
Fragment: Juxtamembrane segment and kinase domain: residues 577-947
Mutation: Y608A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA3, ETK, ETK1, HEK, TYRO4 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P29320, receptor protein-tyrosine kinase
#2: Protein/peptide peptide substrate


Mass: 1429.553 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 1.8 Å3/Da / Density % sol: 30.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 mg/mL Protein, 25% PEG 3350, 0.04M Ammonium sulfate, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.78→34.04 Å / Num. all: 29459 / Num. obs: 29456 / % possible obs: 100 % / Redundancy: 3.6 % / Biso Wilson estimate: 21.842 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 7.855
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.78-1.883.50.2243.31474442660.224100
1.88-1.993.50.1484.81414540360.148100
1.99-2.133.50.1036.61347238190.103100
2.13-2.33.60.0768.91252235050.076100
2.3-2.523.60.05512.31178132740.055100
2.52-2.823.60.04315.21071329550.043100
2.82-3.253.60.03318.4954926200.033100
3.25-3.983.70.04211.9817922370.042100
3.98-5.633.60.04211.5637117510.042100
5.63-34.043.50.03514.134769930.03599.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.85 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.81 Å
Translation2.5 Å27.81 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FXX

3fxx


Resolution: 1.8→26.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.231 / WRfactor Rwork: 0.191 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.87 / SU B: 2.345 / SU ML: 0.076 / SU R Cruickshank DPI: 0.13 / SU Rfree: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1430 5 %RANDOM
Rwork0.179 ---
obs0.181 28393 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.56 Å2 / Biso mean: 29.522 Å2 / Biso min: 11.92 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error free: 0.121 Å
Refinement stepCycle: LAST / Resolution: 1.8→26.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 0 233 2578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222413
X-RAY DIFFRACTIONr_bond_other_d0.0010.021691
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.9643261
X-RAY DIFFRACTIONr_angle_other_deg0.87134116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.415295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.49423.704108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80815444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8781518
X-RAY DIFFRACTIONr_chiral_restr0.0750.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022631
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02488
X-RAY DIFFRACTIONr_nbd_refined0.2090.2484
X-RAY DIFFRACTIONr_nbd_other0.1860.21784
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21202
X-RAY DIFFRACTIONr_nbtor_other0.0820.21191
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2156
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1890.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.218
X-RAY DIFFRACTIONr_mcbond_it1.1171.51916
X-RAY DIFFRACTIONr_mcbond_other0.1791.5593
X-RAY DIFFRACTIONr_mcangle_it1.27122371
X-RAY DIFFRACTIONr_scbond_it2.00231129
X-RAY DIFFRACTIONr_scangle_it2.7234.5887
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 102 -
Rwork0.209 1965 -
all-2067 -
obs--99.52 %

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