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- PDB-1j9o: SOLUTION STRUCTURE OF HUMAN LYMPHOTACTIN -

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Basic information

Entry
Database: PDB / ID: 1j9o
TitleSOLUTION STRUCTURE OF HUMAN LYMPHOTACTIN
ComponentsLYMPHOTACTIN
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 granzyme B production / positive regulation of thymocyte migration / positive regulation of B cell chemotaxis / negative regulation of T cell cytokine production / negative regulation of T-helper 1 type immune response / 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 granzyme B production / positive regulation of thymocyte migration / positive regulation of B cell chemotaxis / negative regulation of T cell cytokine production / negative regulation of T-helper 1 type immune response / positive regulation of natural killer cell chemotaxis / chemokine receptor binding / positive regulation of transforming growth factor beta production / positive regulation of T-helper 1 cell cytokine production / positive regulation of T cell chemotaxis / CCR chemokine receptor binding / positive regulation of T-helper 2 cell cytokine production / positive regulation of leukocyte chemotaxis / negative regulation of CD4-positive, alpha-beta T cell proliferation / chemokine-mediated signaling pathway / positive regulation of CD4-positive, alpha-beta T cell proliferation / eosinophil chemotaxis / chemokine activity / positive regulation of neutrophil chemotaxis / Chemokine receptors bind chemokines / negative regulation of interleukin-2 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / negative regulation of type II interferon production / positive regulation of interleukin-10 production / cellular response to transforming growth factor beta stimulus / release of sequestered calcium ion into cytosol / neutrophil chemotaxis / cellular response to interleukin-4 / positive regulation of release of sequestered calcium ion into cytosol / negative regulation of DNA-binding transcription factor activity / positive regulation of T cell cytokine production / response to virus / positive regulation of T cell mediated cytotoxicity / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / regulation of inflammatory response / G alpha (q) signalling events / positive regulation of cell migration / inflammatory response / 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. / Kitabwalla, M. / Pauza, C.D. / Markley, J.L. / 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 28, 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
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYMPHOTACTIN


Theoretical massNumber of molelcules
Total (without water)10,2871
Polymers10,2871
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 / 50STRUCTURES WITH THE LOWEST ENERGY, TARGET FUNCTION
Representative

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Components

#1: Protein LYMPHOTACTIN


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
Has protein modificationY

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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

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Sample preparation

CrystalDescription: THE STRUCTURE WAS DETERMINED USING TRIPLE- RESONANCE NMR SPECTROSCOPY.
Details
Solution-IDContentsSolvent system
11.3mM human lymphotactin U-15N-13C; 20 mM phosphate buffer, 200mM NaCl90% H2O/10% D2O
21mM human lymphotactin U-15N; 20 mM phosphate buffer, 200mM NaCl90% H2O/10% D2O
31mM human lymphotactin; 20 mM phosphate buffer, 200mM NaCl100% D2O
Sample conditionsIonic strength: 200mM NaCl / pH: 6 / Temperature: 283 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DMXBrukerDMX6002

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Processing

SoftwareName: DYANA / Classification: refinement
NMR software
NameVersionDeveloperClassification
DYANA1.5Guntertrefinement
Felixdata analysis
NMRPipeprocessing
XwinNMRcollection
XEASYdata analysis
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: 1

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