[English] 日本語
Yorodumi
- PDB-1jpa: Crystal Structure of unphosphorylated EphB2 receptor tyrosine kin... -

+
Open data


ID or keywords:

Loading...

-
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 / Ephrin signaling / EPH-Ephrin signaling / hindbrain tangential cell migration / negative regulation of NMDA glutamate receptor activity / vesicle-mediated intercellular transport / EPH-ephrin mediated repulsion of cells / positive regulation of NMDA glutamate receptor activity / EPHB-mediated forward signaling / postsynaptic membrane assembly ...regulation of T-helper 17 type immune response / Ephrin signaling / EPH-Ephrin signaling / hindbrain tangential cell migration / negative regulation of NMDA glutamate receptor activity / vesicle-mediated intercellular transport / EPH-ephrin mediated repulsion of cells / positive regulation of NMDA glutamate receptor activity / EPHB-mediated forward signaling / postsynaptic membrane assembly / optic nerve morphogenesis / urogenital system development / regulation of body fluid levels / tight junction assembly / neuron projection retraction / axon guidance receptor activity / central nervous system projection neuron axonogenesis / negative regulation of axonogenesis / positive regulation of long-term neuronal synaptic plasticity / positive regulation of synaptic plasticity / dendritic spine development / camera-type eye morphogenesis / ephrin receptor activity / regulation of filopodium assembly / positive regulation of dendritic spine morphogenesis / corpus callosum development / regulation of behavioral fear response / regulation of autophagosome assembly / negative regulation of cell adhesion / commissural neuron axon guidance / dendritic spine morphogenesis / negative regulation of Ras protein signal transduction / positive regulation of protein localization to cell surface / axonal fasciculation / positive regulation of synapse assembly / regulation of receptor signaling pathway via JAK-STAT / positive regulation of immunoglobulin production / inner ear morphogenesis / regulation of axonogenesis / retinal ganglion cell axon guidance / regulation of synapse assembly / roof of mouth development / regulation of blood coagulation / B cell activation / regulation of neuronal synaptic plasticity / ephrin receptor signaling pathway / negative regulation of cytokine production involved in inflammatory response / negative regulation of protein phosphorylation / phosphorylation / positive regulation of B cell proliferation / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / platelet-derived growth factor beta-receptor activity / fibroblast growth factor receptor activity / GPI-linked ephrin receptor activity / transmembrane-ephrin receptor activity / insulin-like growth factor receptor activity / axonogenesis / hippocampal mossy fiber to CA3 synapse / axon guidance / hepatocyte growth factor receptor activity / learning / positive regulation of long-term synaptic potentiation / animal organ morphogenesis / cell surface receptor protein tyrosine kinase signaling pathway / epidermal growth factor receptor activity / negative regulation of protein kinase activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / cell morphogenesis / negative regulation of ERK1 and ERK2 cascade / cellular response to amyloid-beta / positive regulation of tumor necrosis factor production / histone H2AXY142 kinase activity / signaling receptor activity / histone H3Y41 kinase activity / amyloid-beta binding / presynaptic membrane / protein tyrosine kinase activity / cellular response to lipopolysaccharide / angiogenesis / postsynaptic membrane / dendritic spine / learning or memory / positive regulation of cell migration / axon / signaling receptor binding / neuronal cell body / dendrite / synapse / protein-containing complex binding / glutamatergic synapse / cell surface
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 ...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 / 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
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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more