[English] 日本語
Yorodumi
- PDB-3etp: The crystal structure of the ligand-binding domain of the EphB2 r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3etp
TitleThe crystal structure of the ligand-binding domain of the EphB2 receptor at 2.0 A resolution
ComponentsEphrin type-B receptor 2
KeywordsTRANSFERASE / Eph receptor / tyrosine kinase / Alternative splicing / ATP-binding / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Transmembrane / Tyrosine-protein kinase
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 / EPH-Ephrin signaling / negative regulation of NMDA glutamate receptor activity / hindbrain tangential cell migration / vesicle-mediated intercellular transport / EPH-ephrin mediated repulsion of cells / positive regulation of NMDA glutamate receptor activity / EPHB-mediated forward signaling ...regulation of T-helper 17 type immune response / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / Ephrin signaling / EPH-Ephrin signaling / negative regulation of NMDA glutamate receptor activity / hindbrain tangential cell migration / vesicle-mediated intercellular transport / EPH-ephrin mediated repulsion of cells / positive regulation of NMDA glutamate receptor activity / EPHB-mediated forward signaling / 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 / negative regulation of axonogenesis / positive regulation of long-term neuronal synaptic plasticity / positive regulation of synaptic plasticity / dendritic spine development / corpus callosum development / camera-type eye morphogenesis / ephrin receptor activity / regulation of filopodium assembly / regulation of behavioral fear response / positive regulation of dendritic spine morphogenesis / regulation of autophagosome assembly / commissural neuron axon guidance / dendritic spine morphogenesis / negative regulation of cell adhesion / 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 / inner ear morphogenesis / positive regulation of immunoglobulin production / regulation of synapse assembly / regulation of axonogenesis / retinal ganglion cell axon guidance / roof of mouth development / regulation of blood coagulation / regulation of neuronal synaptic plasticity / B cell activation / ephrin receptor signaling pathway / negative regulation of cytokine production involved in inflammatory response / phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of B cell proliferation / hippocampal mossy fiber to CA3 synapse / axonogenesis / negative regulation of protein phosphorylation / learning / axon guidance / positive regulation of long-term synaptic potentiation / animal organ morphogenesis / positive regulation of protein localization to plasma membrane / negative regulation of protein kinase activity / cell morphogenesis / receptor protein-tyrosine kinase / negative regulation of ERK1 and ERK2 cascade / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / positive regulation of tumor necrosis factor production / signaling receptor activity / presynaptic membrane / amyloid-beta binding / protein tyrosine kinase activity / cellular response to lipopolysaccharide / angiogenesis / postsynaptic membrane / postsynapse / dendritic spine / learning or memory / positive regulation of cell migration / axon / signaling receptor binding / neuronal cell body / glutamatergic synapse / dendrite / synapse / 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 ...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) / 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 / 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-B receptor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGoldgur, Y. / Paavilainen, S. / Nikolov, D.B. / Himanen, J.P.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of the ligand-binding domain of the EphB2 receptor at 2 A resolution.
Authors: Goldgur, Y. / Paavilainen, S. / Nikolov, D. / Himanen, J.P.
History
DepositionOct 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 6, 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 1.4Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ephrin type-B receptor 2


Theoretical massNumber of molelcules
Total (without water)21,4371
Polymers21,4371
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.028, 54.028, 157.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Ephrin type-B receptor 2 / Tyrosine-protein kinase receptor EPH-3 / Neural kinase / Nuk receptor tyrosine kinase / SEK-3


Mass: 21437.211 Da / Num. of mol.: 1 / Fragment: UNP residues 28-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ephb2, Epth3, Nuk, Sek3 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): AD494
References: UniProt: P54763, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO THE AUTHORS, THE ELECTRON DENSITY OF THIS WELL ORDERED RESIDUE DOES NOT FIT PHE. IT IS ...ACCORDING TO THE AUTHORS, THE ELECTRON DENSITY OF THIS WELL ORDERED RESIDUE DOES NOT FIT PHE. IT IS PROBABLY A CLONING ARTEFACT. THE ORIGINAL PLASMID WAS SEQUENCED AND HAD EITHER TTC (PHE) OR ATC (ILE) AT THIS POSITION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 1.2 M Na/K phosphate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→37.13 Å / Num. obs: 15984

-
Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.4.0077refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NUK

1nuk


Resolution: 2→37.11 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.368 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 806 5 %RANDOM
Rwork0.19833 ---
obs0.20134 15163 96.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.247 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å20 Å2
2--1.2 Å20 Å2
3----2.4 Å2
Refinement stepCycle: LAST / Resolution: 2→37.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 0 185 1688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221544
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0851.9312095
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1485186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8223.15876
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22215253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8391513
X-RAY DIFFRACTIONr_chiral_restr0.1760.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211199
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_it1.5391.5933
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7121514
X-RAY DIFFRACTIONr_scbond_it3.4773611
X-RAY DIFFRACTIONr_scangle_it5.5684.5581
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 39 -
Rwork0.26 872 -
obs--77.27 %

+
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