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- PDB-2qbx: EphB2/SNEW Antagonistic Peptide Complex -

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Basic information

Entry
Database: PDB / ID: 2qbx
TitleEphB2/SNEW Antagonistic Peptide Complex
Components
  • Ephrin type-B receptor 2
  • antagonistic peptide
KeywordsSIGNALING PROTEIN / Receptor tyrosine kinase / bi-directional signaling / tumorigenesis / angiogenesis / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D
Function / homology
Function and homology information


regulation of T-helper 17 type immune response / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / negative regulation of NMDA glutamate receptor activity / hindbrain tangential cell migration / L1CAM interactions / vesicle-mediated intercellular transport / positive regulation of NMDA glutamate receptor activity / postsynaptic membrane assembly / urogenital system development / regulation of body fluid levels ...regulation of T-helper 17 type immune response / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / negative regulation of NMDA glutamate receptor activity / hindbrain tangential cell migration / L1CAM interactions / vesicle-mediated intercellular transport / positive regulation of NMDA glutamate receptor activity / postsynaptic membrane assembly / urogenital system development / regulation of body fluid levels / optic nerve morphogenesis / tight junction assembly / neuron projection retraction / axon guidance receptor activity / central nervous system projection neuron axonogenesis / negative regulation of axonogenesis / regulation of behavioral fear response / transmembrane-ephrin receptor activity / positive regulation of long-term neuronal synaptic plasticity / regulation of autophagosome assembly / positive regulation of dendritic spine morphogenesis / dendritic spine development / corpus callosum development / positive regulation of synaptic plasticity / camera-type eye morphogenesis / regulation of filopodium assembly / negative regulation of Ras protein signal transduction / positive regulation of protein localization to cell surface / commissural neuron axon guidance / dendritic spine morphogenesis / negative regulation of cell adhesion / retinal ganglion cell axon guidance / axonal fasciculation / positive regulation of synapse assembly / EPH-Ephrin signaling / regulation of receptor signaling pathway via JAK-STAT / Ephrin signaling / inner ear morphogenesis / regulation of neuronal synaptic plasticity / B cell activation / roof of mouth development / regulation of blood coagulation / positive regulation of immunoglobulin production / EPH-ephrin mediated repulsion of cells / negative regulation of cytokine production involved in inflammatory response / ephrin receptor signaling pathway / positive regulation of B cell proliferation / EPHB-mediated forward signaling / hippocampal mossy fiber to CA3 synapse / negative regulation of protein phosphorylation / learning / positive regulation of long-term synaptic potentiation / axon guidance / positive regulation of protein localization to plasma membrane / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / positive regulation of tumor necrosis factor production / presynaptic membrane / nervous system development / amyloid-beta binding / postsynaptic membrane / postsynapse / angiogenesis / protein tyrosine kinase activity / cellular response to lipopolysaccharide / dendritic spine / learning or memory / positive regulation of cell migration / axon / phosphorylation / signaling receptor binding / dendrite / neuronal cell body / glutamatergic synapse / protein-containing complex binding / positive regulation of gene expression / 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 / 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 2, ligand binding domain / 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 / Sterile alpha motif/pointed domain superfamily / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type III domain / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ephrin type-B receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChrencik, J.E. / Brooun, A. / Recht, M.I. / Nicola, G. / Pasquale, E.B. / Kuhn, P. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D)
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Three-dimensional structure of the EphB2 receptor in complex with an antagonistic peptide reveals a novel mode of inhibition.
Authors: Chrencik, J.E. / Brooun, A. / Recht, M.I. / Nicola, G. / Davis, L.K. / Abagyan, R. / Widmer, H. / Pasquale, E.B. / Kuhn, P.
History
DepositionJun 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ephrin type-B receptor 2
B: Ephrin type-B receptor 2
D: antagonistic peptide
P: antagonistic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,49616
Polymers50,3434
Non-polymers1,15312
Water3,135174
1
A: Ephrin type-B receptor 2
P: antagonistic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5566
Polymers25,1712
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ephrin type-B receptor 2
D: antagonistic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,94010
Polymers25,1712
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.183, 40.183, 235.025
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Detailsthe biological unit is a dimer.

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Components

#1: Protein Ephrin type-B receptor 2 / Tyrosine-protein kinase receptor EPH-3


Mass: 23664.738 Da / Num. of mol.: 2 / Fragment: EphB2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHB2, DRT, EPHT3, EPTH3, ERK, HEK5, TYRO5 / Plasmid: pBac6 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): HI-5
References: UniProt: P29323, receptor protein-tyrosine kinase
#2: Protein/peptide antagonistic peptide


Mass: 1506.663 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Antagonistic Peptide
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 100 mM Hepes, pH 7.2, 100 mM ammonium sulfate, and 20% PEG-3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2006 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.299→34.79 Å / Num. all: 17391 / Num. obs: 17391 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.299→2.3 Å / % possible all: 87.06

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NUK

1nuk


Resolution: 2.3→34.79 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.896 / SU B: 10.396 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.395 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2695 942 5.1 %RANDOM
Rwork0.19424 ---
obs0.19793 17391 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.547 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.12 Å20 Å2
2--0.23 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2988 0 60 174 3222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223130
X-RAY DIFFRACTIONr_bond_other_d0.0020.022651
X-RAY DIFFRACTIONr_angle_refined_deg2.1061.9424261
X-RAY DIFFRACTIONr_angle_other_deg1.29536150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg19.4325373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72423.467150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25415488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1221521
X-RAY DIFFRACTIONr_chiral_restr0.2170.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023442
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
X-RAY DIFFRACTIONr_nbd_refined0.1990.2523
X-RAY DIFFRACTIONr_nbd_other0.2070.22765
X-RAY DIFFRACTIONr_nbtor_refined0.1950.21455
X-RAY DIFFRACTIONr_nbtor_other0.0970.21828
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2176
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0680.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.10.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3380.210
X-RAY DIFFRACTIONr_mcbond_it0.9391.52003
X-RAY DIFFRACTIONr_mcbond_other0.1781.5760
X-RAY DIFFRACTIONr_mcangle_it1.41623012
X-RAY DIFFRACTIONr_scbond_it1.83431437
X-RAY DIFFRACTIONr_scangle_it2.6634.51246
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 71 -
Rwork0.235 1174 -
obs--87.06 %

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