[English] 日本語
Yorodumi
- PDB-7kpl: Crystal structure of hEphB1 in apo form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kpl
TitleCrystal structure of hEphB1 in apo form
ComponentsEphrin type-B receptor 1
KeywordsTRANSFERASE / HEPHB1
Function / homology
Function and homology information


skeletal muscle satellite cell activation / hindbrain tangential cell migration / negative regulation of skeletal muscle satellite cell proliferation / optic nerve morphogenesis / central nervous system projection neuron axonogenesis / axon guidance receptor activity / negative regulation of satellite cell differentiation / transmembrane-ephrin receptor activity / immunological synapse formation / filopodium tip ...skeletal muscle satellite cell activation / hindbrain tangential cell migration / negative regulation of skeletal muscle satellite cell proliferation / optic nerve morphogenesis / central nervous system projection neuron axonogenesis / axon guidance receptor activity / negative regulation of satellite cell differentiation / transmembrane-ephrin receptor activity / immunological synapse formation / filopodium tip / dendritic spine development / camera-type eye morphogenesis / dendritic spine morphogenesis / retinal ganglion cell axon guidance / EPH-Ephrin signaling / regulation of JNK cascade / positive regulation of synapse assembly / Ephrin signaling / neural precursor cell proliferation / establishment of cell polarity / cell-substrate adhesion / detection of temperature stimulus involved in sensory perception of pain / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / regulation of ERK1 and ERK2 cascade / neurogenesis / EPHB-mediated forward signaling / axon guidance / cell chemotaxis / receptor protein-tyrosine kinase / modulation of chemical synaptic transmission / protein autophosphorylation / early endosome membrane / angiogenesis / membrane raft / axon / dendrite / protein-containing complex binding / glutamatergic synapse / endoplasmic reticulum / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytosol
Similarity search - Function
Ephrin type-B receptor 1, ligand binding domain / EphB1 , SAM 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. ...Ephrin type-B receptor 1, ligand binding domain / EphB1 , SAM 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 / EGF-like domain signature 2. / 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 / 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
Similarity search - Domain/homology
Ephrin type-B receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.705 Å
AuthorsAhmed, M. / Wang, P. / Sadek, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Identification of tetracycline combinations as EphB1 tyrosine kinase inhibitors for treatment of neuropathic pain.
Authors: Ahmed, M.S. / Wang, P. / Nguyen, N.U.N. / Nakada, Y. / Menendez-Montes, I. / Ismail, M. / Bachoo, R. / Henkemeyer, M. / Sadek, H.A. / Kandil, E.S.
History
DepositionNov 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ephrin type-B receptor 1


Theoretical massNumber of molelcules
Total (without water)31,8231
Polymers31,8231
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.057, 91.461, 97.436
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ephrin type-B receptor 1 / ELK / EPH tyrosine kinase 2 / EPH-like kinase 6 / hEK6 / Neuronally-expressed EPH-related tyrosine ...ELK / EPH tyrosine kinase 2 / EPH-like kinase 6 / hEK6 / Neuronally-expressed EPH-related tyrosine kinase / NET / Tyrosine-protein kinase receptor EPH-2


Mass: 31823.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHB1, ELK, EPHT2, HEK6, NET / Production host: Escherichia coli (E. coli)
References: UniProt: P54762, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium malonate, pH 4.6, 14% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2020
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 8602 / % possible obs: 99.7 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.36 / Net I/σ(I): 9.69
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 1.16 / Num. unique obs: 833 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3zfx

3zfx


Resolution: 2.705→48.718 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 403 4.8 %
Rwork0.1997 7998 -
obs0.202 8401 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.24 Å2 / Biso mean: 35.803 Å2 / Biso min: 14.75 Å2
Refinement stepCycle: final / Resolution: 2.705→48.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 0 36 2092
Biso mean---36.78 -
Num. residues----256
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.705-3.09610.25271120.2252253695
3.0961-3.90060.25841620.2021264499
3.9006-48.70.24121290.1894281899

+
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