[English] 日本語
Yorodumi
- PDB-1kgy: Crystal Structure of the EphB2-ephrinB2 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kgy
TitleCrystal Structure of the EphB2-ephrinB2 complex
Components
  • EPHRIN TYPE-B RECEPTOR 2
  • EPHRIN-B2
KeywordsTRANSFERASE/TRANSFERASE RECEPTOR / Developmental protein / TRANSFERASE-TRANSFERASE RECEPTOR COMPLEX
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 / venous blood vessel morphogenesis / EPHB-mediated forward signaling ...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 / venous blood vessel morphogenesis / EPHB-mediated forward signaling / positive regulation of NMDA glutamate receptor activity / nephric duct morphogenesis / regulation of body fluid levels / urogenital system development / optic nerve morphogenesis / tight junction assembly / postsynaptic membrane assembly / positive regulation of aorta morphogenesis / positive regulation of cardiac muscle cell differentiation / neuron projection retraction / ephrin receptor activity / axon guidance receptor activity / central nervous system projection neuron axonogenesis / negative regulation of axonogenesis / positive regulation of long-term neuronal synaptic plasticity / presynapse assembly / regulation of autophagosome assembly / positive regulation of dendritic spine morphogenesis / dendritic spine development / lymph vessel development / positive regulation of synaptic plasticity / corpus callosum development / regulation of filopodium assembly / camera-type eye morphogenesis / regulation of chemotaxis / regulation of behavioral fear response / transmembrane-ephrin receptor activity / commissural neuron axon guidance / positive regulation of protein localization to cell surface / negative regulation of cell adhesion / dendritic spine morphogenesis / negative regulation of Ras protein signal transduction / regulation of postsynaptic neurotransmitter receptor internalization / cell migration involved in sprouting angiogenesis / axonal fasciculation / positive regulation of synapse assembly / adherens junction organization / regulation of receptor signaling pathway via JAK-STAT / blood vessel morphogenesis / positive regulation of immunoglobulin production / regulation of synapse assembly / inner ear morphogenesis / regulation of axonogenesis / retinal ganglion cell axon guidance / B cell activation / roof of mouth development / regulation of postsynaptic membrane neurotransmitter receptor levels / regulation of neuronal synaptic plasticity / regulation of blood coagulation / keratinocyte proliferation / negative regulation of cytokine production involved in inflammatory response / ephrin receptor signaling pathway / negative regulation of keratinocyte proliferation / positive regulation of B cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / T cell costimulation / ephrin receptor binding / hippocampal mossy fiber to CA3 synapse / axonogenesis / negative regulation of protein phosphorylation / learning / positive regulation of long-term synaptic potentiation / positive regulation of protein localization to plasma membrane / adherens junction / animal organ morphogenesis / postsynaptic density membrane / axon guidance / negative regulation of protein kinase activity / Schaffer collateral - CA1 synapse / 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 / negative regulation of neuron projection development / presynaptic membrane / signaling receptor activity / amyloid-beta binding / postsynapse / cellular response to lipopolysaccharide / postsynaptic membrane / protein tyrosine kinase activity / angiogenesis / dendritic spine / learning or memory / cell adhesion / positive regulation of cell migration / phosphorylation / axon
Similarity search - Function
Ephrin type-B receptor 2, ligand binding domain / Ephrin-B ectodomain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like ...Ephrin type-B receptor 2, ligand binding domain / Ephrin-B ectodomain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / 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 / Cupredoxins - blue copper proteins / Sterile alpha motif/pointed domain superfamily / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type III domain / Cupredoxin / 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 / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ephrin-B2 / Ephrin type-B receptor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsHimanen, J.P. / Rajashankar, K.R. / Lackmann, M. / Cowan, C.A. / Henkemeyer, M. / Nikolov, D.B.
CitationJournal: Nature / Year: 2001
Title: Crystal structure of an Eph receptor-ephrin complex.
Authors: Himanen, J.P. / Rajashankar, K.R. / Lackmann, M. / Cowan, C.A. / Henkemeyer, M. / Nikolov, D.B.
History
DepositionNov 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2017Group: Structure summary

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EPHRIN TYPE-B RECEPTOR 2
B: EPHRIN TYPE-B RECEPTOR 2
C: EPHRIN TYPE-B RECEPTOR 2
D: EPHRIN TYPE-B RECEPTOR 2
E: EPHRIN-B2
F: EPHRIN-B2
G: EPHRIN-B2
H: EPHRIN-B2


Theoretical massNumber of molelcules
Total (without water)146,2908
Polymers146,2908
Non-polymers00
Water00
1
A: EPHRIN TYPE-B RECEPTOR 2
D: EPHRIN TYPE-B RECEPTOR 2
E: EPHRIN-B2
H: EPHRIN-B2


Theoretical massNumber of molelcules
Total (without water)73,1454
Polymers73,1454
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EPHRIN TYPE-B RECEPTOR 2
C: EPHRIN TYPE-B RECEPTOR 2
F: EPHRIN-B2
G: EPHRIN-B2


Theoretical massNumber of molelcules
Total (without water)73,1454
Polymers73,1454
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-36 kcal/mol
Surface area28360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78, 78, 78
Angle α, β, γ (deg.)69, 75, 69
Int Tables number1
Space group name H-MP1
Detailschains B and F form a heterodimer chains C and D form a heterodimer Chains B, C, F, and G form a proposed heterotetramer

-
Components

#1: Protein
EPHRIN TYPE-B RECEPTOR 2


Mass: 20856.512 Da / Num. of mol.: 4 / Fragment: ligand-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P54763, EC: 2.7.1.112
#2: Protein
EPHRIN-B2


Mass: 15715.984 Da / Num. of mol.: 4 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P52800

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6 M Na/K Phosphate, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mg/mlprotein1drop
210 mM1dropKCl
32 mM1dropMgCl2
410 mMHEPES1droppH7.2
51.6 Msodium potassium phospahte1reservoir
6100 mMHEPES-NaOH1reservoirpH7.5

-
Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 1, 2000
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. all: 43549 / Num. obs: 42156 / % possible obs: 96.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.073
Reflection shellResolution: 2.7→2.82 Å / Rmerge(I) obs: 0.37 / % possible all: 93.5

-
Processing

Software
NameClassification
MARdata collection
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
MARdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.7→25 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2956 2581 random
Rwork0.2427 --
all-43465 -
obs-42787 -
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10260 0 0 0 10260
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0082
X-RAY DIFFRACTIONx_angle_deg1.6374
Refinement
*PLUS
Rfactor obs: 0.243 / Rfactor Rfree: 0.295
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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://pdbjlvh1.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