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- PDB-1shw: EphB2 / EphrinA5 Complex Structure -

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Basic information

Entry
Database: PDB / ID: 1shw
TitleEphB2 / EphrinA5 Complex Structure
Components
  • Ephrin type-B receptor 2
  • Ephrin-A5
Keywordshormone/growth factor/receptor / receptor tyrosine kinase / ephrin signaling / hormone-growth factor-receptor COMPLEX
Function / homology
Function and homology information


neurotrophin TRKB receptor binding / regulation of T-helper 17 type immune response / Ephrin signaling / EPH-Ephrin signaling / hindbrain tangential cell migration / EPHA-mediated growth cone collapse / negative regulation of glutamate receptor signaling pathway / vesicle-mediated intercellular transport / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling ...neurotrophin TRKB receptor binding / regulation of T-helper 17 type immune response / Ephrin signaling / EPH-Ephrin signaling / hindbrain tangential cell migration / EPHA-mediated growth cone collapse / negative regulation of glutamate receptor signaling pathway / vesicle-mediated intercellular transport / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / optic nerve morphogenesis / urogenital system development / postsynaptic membrane assembly / tight junction assembly / regulation of body fluid levels / neuron projection retraction / negative regulation of substrate adhesion-dependent cell spreading / ephrin receptor activity / axon guidance receptor activity / central nervous system projection neuron axonogenesis / negative regulation of axonogenesis / synaptic membrane adhesion / positive regulation of long-term neuronal synaptic plasticity / collateral sprouting / cellular response to follicle-stimulating hormone stimulus / dendritic spine development / positive regulation of synaptic plasticity / camera-type eye morphogenesis / regulation of filopodium assembly / corpus callosum development / positive regulation of dendritic spine morphogenesis / positive regulation of collateral sprouting / regulation of behavioral fear response / regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of glutamate receptor signaling pathway / regulation of autophagosome assembly / negative regulation of cell adhesion / chemorepellent activity / commissural neuron axon guidance / dendritic spine morphogenesis / negative regulation of Ras protein signal transduction / positive regulation of protein localization to cell surface / regulation of cell morphogenesis / axonal fasciculation / positive regulation of synapse assembly / regulation of receptor signaling pathway via JAK-STAT / regulation of GTPase activity / inner ear morphogenesis / regulation of focal adhesion assembly / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of immunoglobulin production / regulation of axonogenesis / phosphorylation / retinal ganglion cell axon guidance / regulation of synapse assembly / regulation of blood coagulation / regulation of cell-cell adhesion / roof of mouth development / B cell activation / regulation of neuronal synaptic plasticity / basement membrane / ephrin receptor signaling pathway / ephrin receptor binding / positive regulation of B cell proliferation / neuron projection maintenance / negative regulation of cytokine production involved in inflammatory response / cellular response to forskolin / regulation of microtubule cytoskeleton organization / axonogenesis / axon guidance / hippocampal mossy fiber to CA3 synapse / cell surface receptor protein tyrosine kinase signaling pathway / learning / positive regulation of long-term synaptic potentiation / animal organ morphogenesis / cell periphery / GABA-ergic synapse / adherens junction / regulation of actin cytoskeleton organization / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / negative regulation of ERK1 and ERK2 cascade / receptor protein-tyrosine kinase / cell morphogenesis / peptidyl-tyrosine phosphorylation / caveola
Similarity search - Function
Ephrin type-B receptor 2, ligand binding domain / Ephrin-A 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-A 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 / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
triacetyl-beta-chitotriose / Ephrin-A5 / Ephrin type-B receptor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHimanen, J.P. / Chumley, M.J. / Lackmann, M. / Li, C. / Barton, W.A. / Jeffrey, P.D. / Vearing, C. / Geleick, D. / Feldheim, D.A. / Boyd, A.W.
CitationJournal: Nat.Neurosci. / Year: 2004
Title: Repelling class discrimination: ephrin-A5 binds to and activates EphB2 receptor signaling
Authors: Himanen, J.P. / Chumley, M.J. / Lackmann, M. / Li, C. / Barton, W.A. / Jeffrey, P.D. / Vearing, C. / Geleick, D. / Feldheim, D.A. / Boyd, A.W. / Henkemeyer, M. / Nikolov, D.B.
History
DepositionFeb 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ephrin-A5
B: Ephrin type-B receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8984
Polymers37,2052
Non-polymers6932
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.89, 88.97, 122.81
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ephrin-A5 / EPH-related receptor tyrosine kinase ligand 7 / LERK-7 / AL-1


Mass: 16320.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: EFNA5, EPLG7, LERK7, EPL7 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O08543
#2: Protein Ephrin type-B receptor 2 / Tyrosine-protein kinase receptor EPH-3 / Neural kinase / Nuk receptor tyrosine kinase / SEK-3


Mass: 20884.564 Da / Num. of mol.: 1
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 (DE3) / References: UniProt: P54763
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 3350, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 1, 2003
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 21816 / Num. obs: 21147 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.8
Reflection shellResolution: 2→2.09 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EphB2/ EphrinB2

Resolution: 2.2→8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.305 1050 RANDOM
Rwork0.258 --
all-21816 -
obs-21147 -
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2615 0 43 222 2880
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.37

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