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- PDB-1jpa: Crystal Structure of unphosphorylated EphB2 receptor tyrosine kin... -

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Basic information

Entry
Database: PDB / ID: 1jpa
TitleCrystal Structure of unphosphorylated EphB2 receptor tyrosine kinase and juxtamembrane region
Componentsneural kinase, Nuk=Eph/Elk/Eck family receptor-like tyrosine kinase
KeywordsTRANSFERASE / receptor tyrosine kinase / autoinhibited / unphosphorylated / juxtamembrane
Function / homology
Function and homology information


regulation of T-helper 17 type immune response / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / Ephrin signaling / negative regulation of NMDA glutamate receptor activity / EPH-Ephrin signaling / hindbrain tangential cell migration / vesicle-mediated intercellular transport / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / positive regulation of NMDA glutamate receptor activity ...regulation of T-helper 17 type immune response / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / Ephrin signaling / negative regulation of NMDA glutamate receptor activity / EPH-Ephrin signaling / hindbrain tangential cell migration / vesicle-mediated intercellular transport / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / positive regulation of NMDA glutamate receptor activity / regulation of body fluid levels / urogenital system development / postsynaptic membrane assembly / optic nerve morphogenesis / tight junction assembly / neuron projection retraction / axon guidance receptor activity / central nervous system projection neuron axonogenesis / transmembrane-ephrin receptor activity / positive regulation of long-term neuronal synaptic plasticity / negative regulation of axonogenesis / regulation of autophagosome assembly / positive regulation of dendritic spine morphogenesis / dendritic spine development / corpus callosum development / positive regulation of synaptic plasticity / regulation of filopodium assembly / ephrin receptor activity / camera-type eye morphogenesis / regulation of behavioral fear response / negative regulation of Ras protein signal transduction / positive regulation of protein localization to cell surface / commissural neuron axon guidance / dendritic spine morphogenesis / negative regulation of cell adhesion / retinal ganglion cell axon guidance / axonal fasciculation / positive regulation of synapse assembly / regulation of receptor signaling pathway via JAK-STAT / regulation of synapse assembly / inner ear morphogenesis / regulation of axonogenesis / B cell activation / roof of mouth development / regulation of neuronal synaptic plasticity / regulation of blood coagulation / positive regulation of immunoglobulin production / negative regulation of cytokine production involved in inflammatory response / ephrin receptor signaling pathway / positive regulation of B cell proliferation / hippocampal mossy fiber to CA3 synapse / axonogenesis / negative regulation of protein phosphorylation / learning / positive regulation of long-term synaptic potentiation / axon guidance / positive regulation of protein localization to plasma membrane / animal organ morphogenesis / negative regulation of protein kinase activity / cell morphogenesis / negative regulation of ERK1 and ERK2 cascade / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of tumor necrosis factor production / presynaptic membrane / signaling receptor activity / amyloid-beta binding / postsynapse / postsynaptic membrane / protein tyrosine kinase activity / angiogenesis / cellular response to lipopolysaccharide / dendritic spine / learning or memory / positive regulation of cell migration / axon / phosphorylation / signaling receptor binding / neuronal cell body / synapse / glutamatergic synapse / dendrite / protein-containing complex binding / positive regulation of gene expression / cell surface / nucleoplasm / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Ephrin type-B receptor 2, 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-B receptor 2, 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 / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Ephrin type-B receptor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsWybenga-Groot, L.E. / Pawson, T. / Sicheri, F.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: Structural basis for autoinhibition of the Ephb2 receptor tyrosine kinase by the unphosphorylated juxtamembrane region.
Authors: Wybenga-Groot, L.E. / Baskin, B. / Ong, S.H. / Tong, J. / Pawson, T. / Sicheri, F.
History
DepositionAug 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 600HETEROGEN ONLY THE ADENINE RING OF ANP (AMP-PNP), PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, WAS ...HETEROGEN ONLY THE ADENINE RING OF ANP (AMP-PNP), PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, WAS SEEN IN THE DENSITY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: neural kinase, Nuk=Eph/Elk/Eck family receptor-like tyrosine kinase
B: neural kinase, Nuk=Eph/Elk/Eck family receptor-like tyrosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6614
Polymers70,6492
Non-polymers1,0122
Water4,684260
1
A: neural kinase, Nuk=Eph/Elk/Eck family receptor-like tyrosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8312
Polymers35,3241
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: neural kinase, Nuk=Eph/Elk/Eck family receptor-like tyrosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8312
Polymers35,3241
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.052, 57.616, 67.742
Angle α, β, γ (deg.)112.95, 103.17, 91.58
Int Tables number1
Space group name H-MP1

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Components

#1: Protein neural kinase, Nuk=Eph/Elk/Eck family receptor-like tyrosine kinase


Mass: 35324.465 Da / Num. of mol.: 2 / Fragment: partial juxtamembrane, entire kinase domain / Mutation: Y604F, Y610F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P54763
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 301 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HEPES, magnesium chloride, PEG 4000, isopropanol, ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 301K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112.5 mg/mlprotein1drop
20.1 MHEPES1reservoir
30.2 M1reservoirMgCl2
410 %(w/v)PEG40001reservoir
510 %(v/v)isopropanol1reservoir
615 %(v/v)ethylene glycol1reservoir

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-D10.9790, 0.9788, 0.9770
SYNCHROTRONAPS 14-BM-C21
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMay 28, 2000
ADSC QUANTUM 42CCDSep 21, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97881
30.9771
411
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 43865 / % possible obs: 90.3 % / Num. measured all: 80035 / Rmerge(I) obs: 0.033
Reflection shell
*PLUS
% possible obs: 55.9 % / Rmerge(I) obs: 0.146

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo-form from MAD data

Resolution: 1.91→25.65 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.27 4050 10 %random
Rwork0.231 ---
obs-39931 --
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.91→25.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4361 0 20 260 4641
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.09
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.73
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Num. reflection all: 42903 / σ(F): 2 / % reflection Rfree: 8.7 % / Rfactor all: 0.241 / Rfactor obs: 0.231 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

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