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- PDB-1g2t: SOLUTION STRUCTURE OF EOTAXIN-3 -

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Basic information

Entry
Database: PDB / ID: 1g2t
TitleSOLUTION STRUCTURE OF EOTAXIN-3
ComponentsEOTAXIN-3
KeywordsCYTOKINE / beta-beta-beta-alpha helix
Function / homology
Function and homology information


CCR3 chemokine receptor binding / CX3C chemokine receptor binding / CCR chemokine receptor binding / lymphocyte chemotaxis / positive regulation of chemotaxis / T cell chemotaxis / eosinophil chemotaxis / chemokine-mediated signaling pathway / chemokine activity / positive regulation of actin filament polymerization ...CCR3 chemokine receptor binding / CX3C chemokine receptor binding / CCR chemokine receptor binding / lymphocyte chemotaxis / positive regulation of chemotaxis / T cell chemotaxis / eosinophil chemotaxis / chemokine-mediated signaling pathway / chemokine activity / positive regulation of actin filament polymerization / monocyte chemotaxis / cellular response to interleukin-1 / positive regulation of endothelial cell proliferation / neutrophil chemotaxis / positive regulation of GTPase activity / cellular response to type II interferon / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / receptor ligand activity / positive regulation of ERK1 and ERK2 cascade / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / signal transduction / extracellular space
Similarity search - Function
CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
C-C motif chemokine 26
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry-simulated annealing protocol implemented in XPLOR
Model type detailsminimized average
AuthorsYe, J. / Mayer, K.L. / Mayer, M.R. / Stone, M.J.
CitationJournal: Biochemistry / Year: 2001
Title: NMR solution structure and backbone dynamics of the CC chemokine eotaxin-3.
Authors: Ye, J. / Mayer, K.L. / Mayer, M.R. / Stone, M.J.
History
DepositionOct 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EOTAXIN-3


Theoretical massNumber of molelcules
Total (without water)8,4131
Polymers8,4131
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #PDB ID 1G2Sminimized average structure

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Components

#1: Protein EOTAXIN-3 / / SMALL INDUCIBLE CYTOKINE A26 / MACROPHAGE INFLAMMATORY PROTEIN 4-ALPHA


Mass: 8412.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EOTAXIN-3 / Organ: LUNG / Plasmid: PET28A+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y258

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
13213C, 15N simultaneously edited NOESY
1433D 13C-separated NOESY
15413C-edited HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM eotaxin-3,U-15N, 20mM sodium acetate (deteurated), 90% H2O, 10% D2O90% H2O/10% D2O
22 mM eotaxin-3,U-15N, 13C, 20mM sodium acetate (deteurated), 90% H2O, 10% D2O90% H2O/10% D2O
32 mM eotaxin-3,U-15N, 13C, 20mM sodium acetate (deteurated), 90% H2O, 10% D2O100% D2O
40.5 mM eotaxin-3,10% 13C-labeled, 20mM sodium acetate (deteurated), 100% D2O100% D2O
Sample conditionsIonic strength: 20 mM / pH: 5 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORXPLOR98.1Brungerstructure solution
FelixFelix98msi industrydata analysis
VNMRVNMR6.1Variancollection
Procheck-nmrPROCHECK v.3laskowskistructure solution
Procheck-nmrPROCHECK v.3laskowskirefinement
RefinementMethod: distance geometry-simulated annealing protocol implemented in XPLOR
Software ordinal: 1
Details: The structures are based on a total of 1250 restraints, 1157 are NOE-derived distance constraints, 69 dihedral angle restraints, 17 distance restraints from hydrogn bonds.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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