+Open data
-Basic information
Entry | Database: PDB / ID: 2n54 | ||||||
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Title | Solution structure of a disulfide stabilized XCL1 dimer | ||||||
Components | LymphotactinXCL1 | ||||||
Keywords | CYTOKINE / 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 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 leukocyte 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 / negative regulation of interleukin-2 production / monocyte chemotaxis / positive regulation of interleukin-10 production / negative regulation of type II interferon production / positive regulation of CD8-positive, alpha-beta T cell proliferation / cellular response to interleukin-1 / release of sequestered calcium ion into cytosol / cellular response to transforming growth factor beta stimulus / cellular response to interleukin-4 / 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 / cellular response to type II interferon / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Tyler, R.C. / Tuinstra, R.L. / Peterson, F.F. / Volkman, B.F. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2n54.cif.gz | 956.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2n54.ent.gz | 809.1 KB | Display | PDB format |
PDBx/mmJSON format | 2n54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/2n54 ftp://data.pdbj.org/pub/pdb/validation_reports/n5/2n54 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 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 | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.02 / pH: 6.0 / Pressure: ambient / Temperature: 313 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||||
NMR constraints | NOE 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 representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1 |