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- PDB-2i85: NMR solution structure of Human ephrinB2 ectodomain -

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Basic information

Entry
Database: PDB / ID: 2i85
TitleNMR solution structure of Human ephrinB2 ectodomain
ComponentsEphrin-B2
KeywordsSIGNALING PROTEIN / ephrinB2 ectodomain / NMR solution structure
Function / homology
Function and homology information


venous blood vessel morphogenesis / nephric duct morphogenesis / positive regulation of aorta morphogenesis / positive regulation of cardiac muscle cell differentiation / lymph vessel development / regulation of chemotaxis / regulation of postsynaptic neurotransmitter receptor internalization / cell migration involved in sprouting angiogenesis / adherens junction organization / EPH-Ephrin signaling ...venous blood vessel morphogenesis / nephric duct morphogenesis / positive regulation of aorta morphogenesis / positive regulation of cardiac muscle cell differentiation / lymph vessel development / regulation of chemotaxis / regulation of postsynaptic neurotransmitter receptor internalization / cell migration involved in sprouting angiogenesis / adherens junction organization / EPH-Ephrin signaling / blood vessel morphogenesis / Ephrin signaling / regulation of postsynaptic membrane neurotransmitter receptor levels / keratinocyte proliferation / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / negative regulation of keratinocyte proliferation / anatomical structure morphogenesis / T cell costimulation / EPHB-mediated forward signaling / ephrin receptor binding / adherens junction / animal organ morphogenesis / postsynaptic density membrane / axon guidance / Schaffer collateral - CA1 synapse / cell-cell signaling / negative regulation of neuron projection development / presynaptic membrane / virus receptor activity / cell adhesion / focal adhesion / glutamatergic synapse / positive regulation of cell population proliferation / plasma membrane
Similarity search - Function
Ephrin-B ectodomain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like ...Ephrin-B ectodomain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsRan, X. / Fan, J. / Song, J.
CitationJournal: To be published
Title: NMR solution structure of Human ephrinB2 ectodomain
Authors: Ran, X. / Fan, J. / Song, J.
History
DepositionSep 1, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ephrin-B2


Theoretical massNumber of molelcules
Total (without water)16,2051
Polymers16,2051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200target funtion less than 2
RepresentativeModel #1lowest energy

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Components

#1: Protein Ephrin-B2 / EPH-related receptor tyrosine kinase ligand 5 / LERK-5 / HTK ligand / HTK-L


Mass: 16204.536 Da / Num. of mol.: 1 / Fragment: ectodomain, residues 1-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HELA CELLS / Plasmid: PET-32a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P52799

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-edited HSQC-TOCSY
12115N-edited HSQC-NOESY
131HN(CA)CB
141CBCA(CO)NH
151HNCO
16113C-NOESY
272(H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM ephrinB2 ectodomain U-15N,13C; 20mM phosphate buffer(pH 6.8); 90% H2O, 10% D2O90% H2O/10% D2O
20.5mM ephrinB2 ectodomain U-15N,13C; 20mM phosphate buffer(pH 6.8); 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthPressure (kPa)Temperature (K)
16.8 1 atm293 K
26.8 1 atm293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, P.structure solution
NMRPipeDelaglio, F.processing
AmberCase DA et al.refinement
NMRViewJohnson, B.A.data analysis
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target funtion less than 2 / Conformers calculated total number: 200 / Conformers submitted total number: 10

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