[English] 日本語
Yorodumi
- PDB-2wo2: Crystal Structure of the EphA4-ephrinB2 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wo2
TitleCrystal Structure of the EphA4-ephrinB2 complex
Components
  • EPHRIN TYPE-A RECEPTOR
  • EPHRIN-B2
KeywordsTRANSFERASE/SIGNALING PROTEIN / TRANSFERASE-SIGNALING PROTEIN COMPLEX / OSTEOGENESIS / AXON GUIDANCE / CELL SURFACE RECEPTOR / DEVELOPMENTAL PROTEIN / NEUROGENESIS / CELL SIGNALING
Function / homology
Function and homology information


DH domain binding / neuron projection fasciculation / : / negative regulation of proteolysis involved in protein catabolic process / corticospinal tract morphogenesis / regulation of astrocyte differentiation / neuron projection guidance / venous blood vessel morphogenesis / nephric duct morphogenesis / fasciculation of sensory neuron axon ...DH domain binding / neuron projection fasciculation / : / negative regulation of proteolysis involved in protein catabolic process / corticospinal tract morphogenesis / regulation of astrocyte differentiation / neuron projection guidance / venous blood vessel morphogenesis / nephric duct morphogenesis / fasciculation of sensory neuron axon / fasciculation of motor neuron axon / positive regulation of aorta morphogenesis / synapse pruning / negative regulation of cellular response to hypoxia / negative regulation of axon regeneration / positive regulation of cardiac muscle cell differentiation / transmembrane-ephrin receptor activity / glial cell migration / positive regulation of amyloid precursor protein catabolic process / presynapse assembly / PH domain binding / regulation of modification of synaptic structure / GPI-linked ephrin receptor activity / regulation of synapse pruning / lymph vessel development / regulation of chemotaxis / adherens junction organization / positive regulation of dendrite morphogenesis / regulation of dendritic spine morphogenesis / negative regulation of cell adhesion / motor neuron axon guidance / cell migration involved in sprouting angiogenesis / EPH-Ephrin signaling / innervation / blood vessel morphogenesis / Ephrin signaling / adult walking behavior / regulation of GTPase activity / negative regulation of epithelial to mesenchymal transition / Somitogenesis / regulation of axonogenesis / positive regulation of amyloid-beta formation / EPHA-mediated growth cone collapse / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of intracellular signal transduction / negative regulation of long-term synaptic potentiation / cochlea development / keratinocyte proliferation / EPH-ephrin mediated repulsion of cells / anatomical structure morphogenesis / negative regulation of keratinocyte proliferation / ephrin receptor signaling pathway / axonal growth cone / regulation of postsynaptic membrane neurotransmitter receptor levels / ephrin receptor binding / T cell costimulation / axon terminus / EPHB-mediated forward signaling / positive regulation of cell adhesion / axon guidance / protein tyrosine kinase binding / peptidyl-tyrosine phosphorylation / negative regulation of cell migration / animal organ morphogenesis / dendritic shaft / positive regulation of JNK cascade / filopodium / adherens junction / neuromuscular junction / receptor protein-tyrosine kinase / postsynaptic density membrane / negative regulation of ERK1 and ERK2 cascade / Schaffer collateral - CA1 synapse / cellular response to amyloid-beta / kinase activity / cell-cell signaling / negative regulation of neuron projection development / amyloid-beta binding / protein autophosphorylation / cellular response to lipopolysaccharide / presynaptic membrane / virus receptor activity / protein tyrosine kinase activity / early endosome membrane / perikaryon / dendritic spine / negative regulation of neuron apoptotic process / mitochondrial outer membrane / protein kinase activity / cell adhesion / negative regulation of translation / protein stabilization / positive regulation of cell migration / axon / focal adhesion / positive regulation of cell population proliferation / dendrite / glutamatergic synapse / cell surface / ATP binding
Similarity search - Function
Ephrin-B ectodomain / Ephrin type-A receptor 4, SAM domain / Ephrin type-A receptor 4, ligand binding domain / 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 ...Ephrin-B ectodomain / Ephrin type-A receptor 4, SAM domain / Ephrin type-A receptor 4, ligand binding domain / 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 / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Jelly Rolls / Serine/Threonine protein kinases, 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ephrin-B2 / Ephrin type-A receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsBowden, T.A. / Aricescu, A.R. / Nettleship, J.E. / Siebold, C. / Rahman-Huq, N. / Owens, R.J. / Stuart, D.I. / Jones, E.Y.
CitationJournal: Structure / Year: 2009
Title: Structural Plasticity of Eph-Receptor A4 Facilitates Cross-Class Ephrin Signalling
Authors: Bowden, T.A. / Aricescu, A.R. / Nettleship, J.E. / Siebold, C. / Rahman-Huq, N. / Owens, R.J. / Stuart, D.I. / Jones, E.Y.
History
DepositionJul 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 9, 2011Group: Database references
Revision 1.3Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Jul 1, 2020Group: Data collection / Derived calculations / Other / Category: chem_comp / pdbx_database_status / struct_conn
Item: _chem_comp.type / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EPHRIN TYPE-A RECEPTOR
B: EPHRIN-B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1953
Polymers38,9742
Non-polymers2211
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-7.9 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.371, 107.371, 47.619
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein EPHRIN TYPE-A RECEPTOR / TYROSINE-PROTEIN KINASE RECEPTOR SEK / RECEPTOR PROTEIN-TYROSINE KINASE HEK8 / TYROSINE-PROTEIN KINASE TYRO1


Mass: 21467.191 Da / Num. of mol.: 1 / Fragment: EPHRIN LIGAND BINDING DOMAIN, RESIDUES 30-202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: P54764, receptor protein-tyrosine kinase
#2: Protein EPHRIN-B2 / EPH-RELATED RECEPTOR TYROSINE KINASE LIGAND 5 / LERK-5 / HTK LIGAND / HTK-L


Mass: 17506.854 Da / Num. of mol.: 1 / Fragment: EPH RECEPTOR BINDING DOMAIN, RESIDUES 27-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P52799
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 39.6 % / Description: NONE
Crystal growpH: 6
Details: 30% PEG 6000, 1 M LITHIUM CHLORIDE, AND 100 MM MES PH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.977
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 20, 2006 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 11645 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Biso Wilson estimate: 60.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 43.2
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.6 / % possible all: 94.2

-
Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KGY

1kgy


Resolution: 2.45→28 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / SU B: 26.32 / SU ML: 0.267 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.054 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26021 564 4.9 %RANDOM
Rwork0.21565 ---
obs0.21784 11062 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.394 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å2-0.45 Å20 Å2
2---0.9 Å20 Å2
3---1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.45→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2533 0 14 49 2596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222602
X-RAY DIFFRACTIONr_bond_other_d0.0010.021789
X-RAY DIFFRACTIONr_angle_refined_deg1.0641.9673518
X-RAY DIFFRACTIONr_angle_other_deg0.72734362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2075311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.65125.118127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62815471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1871514
X-RAY DIFFRACTIONr_chiral_restr0.0650.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212861
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02512
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_it0.2951.51557
X-RAY DIFFRACTIONr_mcbond_other0.0361.5636
X-RAY DIFFRACTIONr_mcangle_it0.56122526
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.70431045
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2354.5992
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.451→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.681 35 -
Rwork0.518 774 -
obs--93.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.85840.1795-0.02063.4343-0.94393.34450.08270.15590.1114-0.1691-0.01240.1727-0.0833-0.058-0.07030.07260.0532-0.0070.0792-0.02110.030515.515355.439517.8607
23.8099-0.42021.5683.04261.75883.89330.04860.1773-0.82010.33350.0170.45850.460.0362-0.06550.0731-0.00650.06620.0522-0.06610.32696.239629.913113.1842
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 205
2X-RAY DIFFRACTION2B28 - 167

+
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