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- PDB-1j8i: Solution Structure of Human Lymphotactin -

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Basic information

Entry
Database: PDB / ID: 1j8i
TitleSolution Structure of Human Lymphotactin
ComponentsLymphotactinXCL1
KeywordsCYTOKINE / Chemokine
Function / homology
Function and homology information


mature natural killer cell chemotaxis / positive regulation of granzyme A production / negative regulation of T-helper 1 cell activation / positive regulation of immunoglobulin production in mucosal tissue / positive regulation of thymocyte migration / positive regulation of granzyme B production / negative regulation of T-helper 1 type immune response / positive regulation of B cell chemotaxis / negative regulation of T cell cytokine production / positive regulation of natural killer cell chemotaxis ...mature natural killer cell chemotaxis / positive regulation of granzyme A production / negative regulation of T-helper 1 cell activation / positive regulation of immunoglobulin production in mucosal tissue / positive regulation of thymocyte migration / positive regulation of granzyme B production / negative regulation of T-helper 1 type immune response / positive regulation of B cell chemotaxis / negative regulation of T cell cytokine production / positive regulation of natural killer cell chemotaxis / chemokine receptor binding / positive regulation of T-helper 1 cell cytokine production / positive regulation of transforming growth factor beta production / positive regulation of T cell chemotaxis / positive regulation of T-helper 2 cell cytokine production / CCR chemokine receptor binding / lymphocyte chemotaxis / positive regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / eosinophil chemotaxis / chemokine-mediated signaling pathway / positive regulation of neutrophil chemotaxis / Chemokine receptors bind chemokines / chemokine activity / positive regulation of leukocyte chemotaxis / negative regulation of interleukin-2 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / monocyte chemotaxis / positive regulation of interleukin-10 production / negative regulation of type II interferon production / cellular response to interleukin-1 / cellular response to interleukin-4 / release of sequestered calcium ion into cytosol / cellular response to transforming growth factor beta stimulus / neutrophil chemotaxis / positive regulation of release of sequestered calcium ion into cytosol / response to virus / negative regulation of DNA-binding transcription factor activity / positive regulation of T cell cytokine production / cellular response to type II interferon / positive regulation of T cell mediated cytotoxicity / cell-cell signaling / cellular response to tumor necrosis factor / regulation of inflammatory response / G alpha (q) signalling events / positive regulation of ERK1 and ERK2 cascade / inflammatory response / G protein-coupled receptor signaling pathway / negative regulation of DNA-templated transcription / signal transduction / protein homodimerization activity / extracellular space / extracellular region
Similarity search - Function
C chemokine / 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 / torsion angle dynamics
AuthorsKuloglu, E.S. / McCaslin, D.R. / Markley, J.L. / Pauza, C.D. / Volkman, B.F.
CitationJournal: Biochemistry / Year: 2001
Title: Monomeric solution structure of the prototypical 'C' chemokine lymphotactin.
Authors: Kuloglu, E.S. / McCaslin, D.R. / Kitabwalla, M. / Pauza, C.D. / Markley, J.L. / Volkman, B.F.
History
DepositionMay 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2001Provider: 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

Downloads & links

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Assembly

Deposited unit
A: Lymphotactin


Theoretical massNumber of molelcules
Total (without water)10,2871
Polymers10,2871
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 / 50structures with the lowest energy, target function
Representative

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Components

#1: Protein Lymphotactin / XCL1


Mass: 10286.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P47992

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
1332D NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.3mM Human Lymphotactin, U-15N,13C; 20 mM phosphate buffer pH 6.0, 200 mM NaCl90% H2O/10% D2O
21 mM Human Lymphotactin, U-15N; 20 mM phosphate buffer pH 6.0, 200 mM NaCl90% H2O/10% D2O
31 mM Human Lymphotactin, 20 mM phosphate buffer pH 6.0, 200 mM NaCl100% D2O
Sample conditionsIonic strength: 200 mM sodium chloride / pH: 6.0 / Temperature: 283 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntertstructure solution
NMRPipeprocessing
XwinNMRcollection
Felixprocessing
XEASYdata analysis
DYANAGuntertrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structures are based on a total of 1258 NOE-derived distance constraints, 60 dihedral angle constraints and 4 disulfide bond constraints.
NMR ensembleConformer selection criteria: structures with the lowest energy, target function
Conformers calculated total number: 50 / Conformers submitted total number: 20

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