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- PDB-2n54: Solution structure of a disulfide stabilized XCL1 dimer -

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Basic information

Entry
Database: PDB / ID: 2n54
TitleSolution structure of a disulfide stabilized XCL1 dimer
ComponentsLymphotactin
KeywordsCYTOKINE / XCL1 / dimer / Chemokine / metamorphic / GAG-binding / HIV-1 inhibition / Lymphotactin / ATAC
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 / 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 granzyme B production / positive regulation of thymocyte migration / 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 / positive regulation of leukocyte chemotaxis / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive 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 / negative regulation of interleukin-2 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of interleukin-10 production / negative regulation of type II interferon production / 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 / 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 / molecular dynamics
Model detailslowest energy, model1
AuthorsTyler, R.C. / Tuinstra, R.L. / Peterson, F.F. / Volkman, B.F.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Engineering Metamorphic Chemokine Lymphotactin/XCL1 into the GAG-Binding, HIV-Inhibitory Dimer Conformation.
Authors: Fox, J.C. / Tyler, R.C. / Guzzo, C. / Tuinstra, R.L. / Peterson, F.C. / Lusso, P. / Volkman, B.F.
History
DepositionJul 7, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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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)20,7022
Polymers20,7022
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1876.9 Å2
ΔGint-18 kcal/mol
Surface area10985.1 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 10350.920 Da / Num. of mol.: 2 / Mutation: A57C, A70C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XCL1, LTN, SCYC1 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / 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 1H-15N NOESY
1213D 1H-13C NOESY aliphatic
1313D 1H-13C NOESY aromatic
1413D F1-13C/F3-13C edited NOESY

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] XCL1, 20 mM potassium phosphate, 0.02 % [U-100% 15N] sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMXCL1-1[U-99% 13C; U-99% 15N]1
20 mMpotassium phosphate-21
0.02 %sodium azide-3[U-100% 15N]1
Sample conditionsIonic strength: 0.02 / pH: 6 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
GARANTBartels, Guntert, Billeter and Wuthrichchemical shift assignment
TALOSCornilescu, Delaglio and Baxgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIHrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1456 / NOE intraresidue total count: 380 / NOE long range total count: 748 / NOE medium range total count: 186 / NOE sequential total count: 142 / Protein phi angle constraints total count: 54 / Protein psi angle constraints total count: 54
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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