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- PDB-2hdm: Solution structure of V21C/V59C Lymphotactin/XCL1 -

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Basic information

Entry
Database: PDB / ID: 2hdm
TitleSolution structure of V21C/V59C Lymphotactin/XCL1
ComponentsLymphotactinXCL1
KeywordsCYTOKINE / Lymphotactin / XCL1 / chemokine / conformational restriction
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 / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT.
AuthorsVolkman, B.F. / Tuinstra, R.L. / Peterson, F.C. / Elgin, E.S.
CitationJournal: Biochemistry / Year: 2007
Title: An engineered second disulfide bond restricts lymphotactin/XCL1 to a chemokine-like conformation with XCR1 agonist activity
Authors: Tuinstra, R.L. / Peterson, F.C. / Elgin, E.S. / Pelzek, A.J. / Volkman, B.F.
History
DepositionJun 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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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)10,1961
Polymers10,1961
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Lymphotactin / XCL1 / XCL1 / Cytokine SCM-1 / ATAC / Lymphotaxin / SCM-1-alpha / Small inducible cytokine C1 / XC chemokine ligand 1


Mass: 10195.685 Da / Num. of mol.: 1 / Mutation: V21C, V59C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XCL1, LTN, SCYC1 / Plasmid: pQE308HT / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009[pREP4] / References: UniProt: P47992

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 13C-separated NOESY (AROMATIC)
NMR detailsText: ALL TRIPLE-RESONANCE AND NOESY SPECTRA WERE ACQUIRED USING A CRYOGENIC PROBE

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Sample preparation

DetailsContents: 1 mM CC3 hLtn, U-15N, 13C; 20 mM phospate buffer, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 10 mM / pH: 6.0 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5collection
NMRPipe2004Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., Bax, A.processing
XEASY1.3Bartels, C, Xia, T.-H., Billeter, M., Guntert, P., Wuthrich, K.data analysis
GARANT2.1Bartels, C., Billeter, M., Guntert, P., Wuthrich, K.data analysis
CYANA2.1Herrmann, T., Guntert, P., Wuthrich, K.structure solution
XPLOR-NIH2.9.3Schwieters, C.D., Kuszewski, J.J, Tjandra, N., Clore, G.M.refinement
RefinementMethod: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT.
Software ordinal: 1
Details: STRUCTURES ARE BASED ON A TOTAL OF 1234 NOE CONSTRAINTS ( 418 INTRA, 333 SEQUENTIAL, 153 MEDIUM and 330 LONG RANGE CONSTRAINTS) AND 82 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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