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- PDB-2jp1: Solution structure of the alternative conformation of XCL1/Lympho... -

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Basic information

Entry
Database: PDB / ID: 2jp1
TitleSolution structure of the alternative conformation of XCL1/Lymphotactin
ComponentsLymphotactin
KeywordsCYTOKINE / Lymphotactin / XCL1 / chemokine / structural rearrangement / protein folding
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. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
AuthorsVolkman, B.F. / Tuinstra, R.L. / Peterson, F.C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Interconversion between two unrelated protein folds in the lymphotactin native state
Authors: Tuinstra, R.L. / Peterson, F.C. / Kutlesa, S. / Elgin, E.S. / Kron, M.A. / Volkman, B.F.
History
DepositionApr 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 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 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lymphotactin
B: Lymphotactin


Theoretical massNumber of molelcules
Total (without water)20,5742
Polymers20,5742
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 10286.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XCL1, LTN, SCYC1 / Production host: Escherichia coli (E. coli) / Strain (production host): SG130099[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
1423D 13C-F1-filtered 13C-F3-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM XCL1 U-15N/13C, 20 mM sodium phosphate, 95% H2O, 5% D2O95% H2O/5% D2O
20.6 mM XCL1 U-15N/13C, 0.6 mM XCL1 unlabeled, 20 mM sodium phosphate, 95% H2O, 5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMXCL1[U-100% 13C; U-100% 15N]1
0.6 mMXCL1-1[U-100% 13C; U-100% 15N]2
0.6 mMXCL1-2unlabeled2
Sample conditionsIonic strength: 22 / pH: 6.0 / Pressure: AMBIENT / Temperature: 313 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
Xplor-NIH2.9.3SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M.refinement
XwinNMR3.5Brukercollection
NMRPipe2004Delagio,F. et al.processing
XEASY1.3Eccles, C., Guntert, P., Billeter, M., Wuthrich, K.data analysis
SPSCAN1.1.0R.W. Glaserdata analysis
GARANT2.1C. Bartelsdata analysis
CYANA2.1Guntert, P.structural calculation
RefinementMethod: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Software ordinal: 1
Details: HOMODIMER STRUCTURES ARE BASED ON A TOTAL OF 1295 NOE CONSTRAINTS ( 320 INTRA, 370 SEQUENTIAL, 104 MEDIUM, 420 LONG RANGE and 81 INTERMONOMER CONSTRAINTS) AND 131 PHI AND PSI DIHEDRAL ANGLE ...Details: HOMODIMER STRUCTURES ARE BASED ON A TOTAL OF 1295 NOE CONSTRAINTS ( 320 INTRA, 370 SEQUENTIAL, 104 MEDIUM, 420 LONG RANGE and 81 INTERMONOMER CONSTRAINTS) AND 131 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. CONSTRAINT WERE IN ONE ASSIGNED AND VALIDATED IN ONE MONOMER AND THEN DUPLICATED TO GENERATE A SYMMETRY RELATED CONSTRAINT IN THE SECOND MONOMER. CONSTRAINT TOTALS LISTED ABOVE INCLUDE CONSTRAINTS FROM BOTH MONOMERS.
NMR constraintsNOE constraints total: 1295 / NOE intraresidue total count: 320 / NOE long range total count: 420 / NOE medium range total count: 104 / NOE sequential total count: 370 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 64 / Protein psi angle constraints total count: 65
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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