[English] 日本語
Yorodumi
- PDB-1f0m: MONOMERIC STRUCTURE OF THE HUMAN EPHB2 SAM (STERILE ALPHA MOTIF) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f0m
TitleMONOMERIC STRUCTURE OF THE HUMAN EPHB2 SAM (STERILE ALPHA MOTIF) DOMAIN
ComponentsEPHRIN TYPE-B RECEPTOR 2
KeywordsSIGNALING PROTEIN / SAM domain
Function / homology
Function and homology information


regulation of T-helper 17 type immune response / hindbrain tangential cell migration / negative regulation of glutamate receptor signaling pathway / vesicle-mediated intercellular transport / L1CAM interactions / optic nerve morphogenesis / tight junction assembly / urogenital system development / neuron projection retraction / central nervous system projection neuron axonogenesis ...regulation of T-helper 17 type immune response / hindbrain tangential cell migration / negative regulation of glutamate receptor signaling pathway / vesicle-mediated intercellular transport / L1CAM interactions / optic nerve morphogenesis / tight junction assembly / urogenital system development / neuron projection retraction / central nervous system projection neuron axonogenesis / regulation of body fluid levels / postsynaptic membrane assembly / axon guidance receptor activity / transmembrane-ephrin receptor activity / negative regulation of axonogenesis / positive regulation of long-term neuronal synaptic plasticity / corpus callosum development / dendritic spine development / regulation of filopodium assembly / camera-type eye morphogenesis / positive regulation of dendritic spine morphogenesis / dendritic spine morphogenesis / negative regulation of Ras protein signal transduction / positive regulation of synaptic plasticity / regulation of behavioral fear response / commissural neuron axon guidance / negative regulation of cell adhesion / positive regulation of protein localization to cell surface / positive regulation of glutamate receptor signaling pathway / phosphorylation / axonal fasciculation / EPH-Ephrin signaling / retinal ganglion cell axon guidance / positive regulation of synapse assembly / Ephrin signaling / regulation of receptor signaling pathway via JAK-STAT / inner ear morphogenesis / positive regulation of immunoglobulin production / regulation of blood coagulation / roof of mouth development / B cell activation / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / regulation of neuronal synaptic plasticity / positive regulation of B cell proliferation / peptidyl-tyrosine phosphorylation / neuron projection maintenance / EPHB-mediated forward signaling / negative regulation of cytokine production involved in inflammatory response / axon guidance / hippocampal mossy fiber to CA3 synapse / positive regulation of long-term synaptic potentiation / learning / positive regulation of protein localization to plasma membrane / receptor protein-tyrosine kinase / negative regulation of ERK1 and ERK2 cascade / cellular response to amyloid-beta / positive regulation of tumor necrosis factor production / nervous system development / amyloid-beta binding / cellular response to lipopolysaccharide / protein tyrosine kinase activity / presynaptic membrane / angiogenesis / dendritic spine / learning or memory / postsynaptic membrane / postsynapse / positive regulation of cell migration / signaling receptor binding / axon / neuronal cell body / positive regulation of gene expression / dendrite / protein-containing complex binding / glutamatergic synapse / cell surface / extracellular region / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol
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 / Transcription Factor, Ets-1 / Ephrin cysteine rich domain / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, 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 / Transcription Factor, Ets-1 / Ephrin cysteine rich domain / 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 / Fibronectin type III domain / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / DNA polymerase; domain 1 / 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ephrin type-B receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsThanos, C.D. / Faham, S. / Goodwill, K.E. / Cascio, D. / Phillips, M. / Bowie, J.U.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Monomeric structure of the human EphB2 sterile alpha motif domain.
Authors: Thanos, C.D. / Faham, S. / Goodwill, K.E. / Cascio, D. / Phillips, M. / Bowie, J.U.
History
DepositionMay 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EPHRIN TYPE-B RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)9,4021
Polymers9,4021
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.837, 54.837, 65.545
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein EPHRIN TYPE-B RECEPTOR 2 / EPHB2


Mass: 9401.772 Da / Num. of mol.: 1 / Fragment: EPHB2 RECEPTOR FRAGMENT, SAM DOMAIN / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P29323
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% peg, 70 mM lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 25K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
250 mMHEPES1drop
387.5 mM1dropLi2SO4
415 %PEG60001drop
5100 mMHEPES1reservoir
6175 mM1reservoirLi2SO4
730 %PEG60001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1
DetectorType: OTHER / Detector: CCD / Date: Sep 8, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→500 Å / Num. all: 5449 / Num. obs: 4963 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 31
Reflection shellResolution: 2.2→50 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.048 / Num. unique all: 5273 / % possible all: 91.1
Reflection shell
*PLUS
% possible obs: 91.1 % / Rmerge(I) obs: 0.302

-
Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.264 524 random
Rwork0.243 --
all0.243 5449 -
obs0.243 4963 -
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms566 0 0 113 679
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg2.097
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg

+
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