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- PDB-1b2t: SOLUTION STRUCTURE OF THE CX3C CHEMOKINE DOMAIN OF FRACTALKINE -

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Basic information

Entry
Database: PDB / ID: 1b2t
TitleSOLUTION STRUCTURE OF THE CX3C CHEMOKINE DOMAIN OF FRACTALKINE
ComponentsPROTEIN (FRACTALKINE)
KeywordsCHEMOKINE
Function / homology
Function and homology information


CXCR1 chemokine receptor binding / positive regulation of calcium-independent cell-cell adhesion / negative regulation of glutamate receptor signaling pathway / negative regulation of interleukin-1 alpha production / leukocyte adhesive activation / CX3C chemokine receptor binding / negative regulation of hippocampal neuron apoptotic process / autocrine signaling / synapse pruning / negative regulation of neuron migration ...CXCR1 chemokine receptor binding / positive regulation of calcium-independent cell-cell adhesion / negative regulation of glutamate receptor signaling pathway / negative regulation of interleukin-1 alpha production / leukocyte adhesive activation / CX3C chemokine receptor binding / negative regulation of hippocampal neuron apoptotic process / autocrine signaling / synapse pruning / negative regulation of neuron migration / positive regulation of microglial cell migration / negative regulation of microglial cell activation / regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of transforming growth factor beta1 production / positive regulation of I-kappaB phosphorylation / microglial cell proliferation / CCR chemokine receptor binding / positive regulation of actin filament bundle assembly / lymphocyte chemotaxis / leukocyte migration involved in inflammatory response / integrin activation / angiogenesis involved in wound healing / eosinophil chemotaxis / chemokine-mediated signaling pathway / leukocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / negative regulation of cell-substrate adhesion / negative regulation of interleukin-1 beta production / positive regulation of cell-matrix adhesion / neuron remodeling / positive regulation of neuroblast proliferation / positive chemotaxis / chemoattractant activity / monocyte chemotaxis / negative regulation of interleukin-6 production / negative regulation of apoptotic signaling pathway / negative regulation of tumor necrosis factor production / regulation of neurogenesis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / cellular response to interleukin-1 / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of cell migration / neutrophil chemotaxis / cell chemotaxis / positive regulation of release of sequestered calcium ion into cytosol / cell projection / response to ischemia / positive regulation of smooth muscle cell proliferation / microglial cell activation / regulation of synaptic plasticity / defense response / cytokine-mediated signaling pathway / positive regulation of neuron projection development / cellular response to type II interferon / cell-cell adhesion / neuron cellular homeostasis / positive regulation of inflammatory response / chemotaxis / integrin binding / cell-cell signaling / cellular response to tumor necrosis factor / G alpha (i) signalling events / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / cell adhesion / inflammatory response / neuron projection / immune response / G protein-coupled receptor signaling pathway / signaling receptor binding / neuronal cell body / positive regulation of cell population proliferation / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
CX3C chemokine domain / 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 / RESTRAINED MOLECULAR DYNAMICS-SIMULATED ANNEALING, THE AMBIGUOUS RESTRAINTS FOR ITERATIVE ASSIGNMENT (ARIA) EXTENSION OF NILGES (M.NILGES, J. MOL. BIOL. 245, 645-660, 1995).
AuthorsHandel, T.M. / Mizoue, L.S. / Bazan, J.F. / Johnson, E.C.
CitationJournal: Biochemistry / Year: 1999
Title: Solution structure and dynamics of the CX3C chemokine domain of fractalkine and its interaction with an N-terminal fragment of CX3CR1.
Authors: Mizoue, L.S. / Bazan, J.F. / Johnson, E.C. / Handel, T.M.
History
DepositionDec 1, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (FRACTALKINE)


Theoretical massNumber of molelcules
Total (without water)8,7861
Polymers8,7861
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 / 70LOWEST ENERGY
RepresentativeModel #20

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Components

#1: Protein PROTEIN (FRACTALKINE)


Mass: 8786.228 Da / Num. of mol.: 1 / Fragment: CHEMOKINE DOMAIN
Source method: isolated from a genetically manipulated source
Details: DISULFIDE BETWEEN 8 AND 34 AND 12 AND 50 / Source: (gene. exp.) Homo sapiens (human) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: P78423

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-EDITED
1213D 13C-EDITED
1314D 13C/13C-EDITED NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED PROTEIN.

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Sample preparation

Sample conditionspH: 5.0 / Pressure: 1 atm / Temperature: 295.5 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX600 / Manufacturer: Bruker / Model: DMX600 / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS-SIMULATED ANNEALING, THE AMBIGUOUS RESTRAINTS FOR ITERATIVE ASSIGNMENT (ARIA) EXTENSION OF NILGES (M.NILGES, J. MOL. BIOL. 245, 645-660, 1995).
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JOURNAL CITATION ABOVE
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 70 / Conformers submitted total number: 20

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