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- PDB-1eot: SOLUTION NMR STRUCTURE OF EOTAXIN, MINIMIZED AVERAGE STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1eot
TitleSOLUTION NMR STRUCTURE OF EOTAXIN, MINIMIZED AVERAGE STRUCTURE
ComponentsEOTAXIN
KeywordsCYTOKINE / CHEMOKINE / PROTEIN SYNTHESIS / EOTAXIN / SOLUTION STRUCTURE / CCR3 / EOSINOPHIL
Function / homology
Function and homology information


response to interleukin-13 / CCR3 chemokine receptor binding / chronic inflammatory response / response to interleukin-4 / mast cell chemotaxis / mammary duct terminal end bud growth / CCR chemokine receptor binding / lymphocyte chemotaxis / eosinophil chemotaxis / chemokine-mediated signaling pathway ...response to interleukin-13 / CCR3 chemokine receptor binding / chronic inflammatory response / response to interleukin-4 / mast cell chemotaxis / mammary duct terminal end bud growth / CCR chemokine receptor binding / lymphocyte chemotaxis / eosinophil chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / branching involved in mammary gland duct morphogenesis / chemokine activity / positive regulation of actin filament polymerization / monocyte chemotaxis / cellular response to interleukin-1 / positive regulation of endothelial cell proliferation / cytoskeleton organization / ERK1 and ERK2 cascade / neutrophil chemotaxis / positive regulation of GTPase activity / actin filament organization / response to virus / response to radiation / negative regulation of neurogenesis / cellular response to type II interferon / intracellular calcium ion homeostasis / positive regulation of angiogenesis / chemotaxis / cellular response to tumor necrosis factor / regulation of cell shape / Interleukin-4 and Interleukin-13 signaling / learning or memory / receptor ligand activity / positive regulation of ERK1 and ERK2 cascade / protein dimerization activity / cell adhesion / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / protein phosphorylation / signal transduction / extracellular space / extracellular region
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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsCrump, M.P. / Rajarathnam, K. / Sykes, B.D.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Solution structure of eotaxin, a chemokine that selectively recruits eosinophils in allergic inflammation.
Authors: Crump, M.P. / Rajarathnam, K. / Kim, K.S. / Clark-Lewis, I. / Sykes, B.D.
History
DepositionJun 17, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software / 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_database_status.process_site / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EOTAXIN


Theoretical massNumber of molelcules
Total (without water)8,3811
Polymers8,3811
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)1 / 40STRUCTURES WERE SELECTED WITH NO VIOLATIONS > 0.3 A OR DIHEDRAL ANGLES > 0.5 A AND GOOD COVALENT GEOMETRY.
Representative

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Components

#1: Protein EOTAXIN


Mass: 8380.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: BOTH SYNTHETIC AND RECOMBINANT SAMPLES WERE PREPARED. RECOMBINANT SAMPLES WERE UNIFORMLY LABELLED WITH N15.
Source: (gene. exp.) Homo sapiens (human)
Description: BOTH SYNTHETIC AND RECOMBINANT SAMPLES WERE PREPARED YES
Cell line: BL21 / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P51671

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121NOESY
131TOCSY
141RPESY
15113C-HSQC
16113C-EDITED HMQC-NOESY
17115N-NOESY HSQC
18115N TOCSY HSQC
NMR detailsText: RESONANCE ASSIGNMENTS WERE ACHIEVED USING STANDARD TWO- AND THREE-DIMENSIONAL SEQUENTIAL ASSIGNMENT TECHNIQUES. NMR RESTRAINTS WERE EXTRACTED FROM 50, 75 AND 150 MS NOESY EXPERIMENTS. COUPLING ...Text: RESONANCE ASSIGNMENTS WERE ACHIEVED USING STANDARD TWO- AND THREE-DIMENSIONAL SEQUENTIAL ASSIGNMENT TECHNIQUES. NMR RESTRAINTS WERE EXTRACTED FROM 50, 75 AND 150 MS NOESY EXPERIMENTS. COUPLING CONSTANTS WERE CALCULATED FROM AN HNHA EXPERIMENT WITH UNIFORMLY LABELLED EOTAXIN.

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Sample preparation

DetailsContents: 90% H2O/10% H2O OR 100% D2O. BUFFER ALSO CONTAINED 1MM DSS AND 1MM SODIUM AZIDE.
Sample conditionsIonic strength: 20mM SODIUM ACETATE / pH: 5.00 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITY 600VarianUNITY 6005001
Varian INOVA 500VarianINOVA 5006002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
VNMRstructure solution
X-PLORstructure solution
NMRPipestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STRUCTURES WERE REFINED WITH MULTIPLE ROUNDS OF SIMULATED ANNEALING WITH THE ADDITION OF NEW NOES AND CORRECTION OF UNAMBIGUOUS NOES. PHI ANGLES WERE ONLY ADDED WHEN THEY AGREED WITH THE ...Details: STRUCTURES WERE REFINED WITH MULTIPLE ROUNDS OF SIMULATED ANNEALING WITH THE ADDITION OF NEW NOES AND CORRECTION OF UNAMBIGUOUS NOES. PHI ANGLES WERE ONLY ADDED WHEN THEY AGREED WITH THE PURELY NOE DRIVEN CONVERGENCE OF THAT ANGLE IN INITIAL STRUCTURE CALCULATIONS. OTHER REFINEMENT INFORMATION CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: STRUCTURES WERE SELECTED WITH NO VIOLATIONS > 0.3 A OR DIHEDRAL ANGLES > 0.5 A AND GOOD COVALENT GEOMETRY.
Conformers calculated total number: 40 / Conformers submitted total number: 1

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