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- PDB-1f2l: CRYSTAL STRUCTURE OF CHEMOKINE DOMAIN OF FRACTALKINE -

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Basic information

Entry
Database: PDB / ID: 1f2l
TitleCRYSTAL STRUCTURE OF CHEMOKINE DOMAIN OF FRACTALKINE
ComponentsFRACTALKINE
KeywordsCYTOKINE / CHEMOATTRACTANT / Fractalkine / neurotactin
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MULTIWAVELENGTH ANOMALOUS DIFFRACTION USING SELENOMETHIONINE (SELENIUM) AS ANOMALOUS SCATTERER / Resolution: 2 Å
AuthorsHoover, D.M. / Mizoue, L.S. / Handel, T.M. / Lubkowski, J.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: The crystal structure of the chemokine domain of fractalkine shows a novel quaternary arrangement.
Authors: Hoover, D.M. / Mizoue, L.S. / Handel, T.M. / Lubkowski, J.
History
DepositionMay 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FRACTALKINE
B: FRACTALKINE
C: FRACTALKINE
D: FRACTALKINE


Theoretical massNumber of molelcules
Total (without water)34,6244
Polymers34,6244
Non-polymers00
Water4,756264
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.473, 110.473, 123.994
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe biological assembly is a dimer constructed from chains A and D, and from chains B and C

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Components

#1: Protein
FRACTALKINE / NEUROTACTIN / CX3C MEMBRANE-ANCHORED CHEMOKINE / SMALL INDUCIBLE CYTOKINE D1


Mass: 8656.017 Da / Num. of mol.: 4 / Fragment: CHEMOKINE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PAED4 / Production host: Escherichia coli (E. coli) / References: UniProt: P78423
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 60.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: sodium formate, disodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 3 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
117 mg/mlprotein1drop
24 Msodium formate1reservoir
3100 mMdisodium citrate1reservoir
4water1reservoir0.010ml

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 25, 1999
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2MADMx-ray1
3MADMx-ray1
4MADMx-ray1
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. all: 345321 / Num. obs: 30366 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.4 % / Biso Wilson estimate: 43.2 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 61.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.491 / Num. unique all: 15345 / % possible all: 98.4
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 345321
Reflection shell
*PLUS
% possible obs: 98.4 % / Mean I/σ(I) obs: 3.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SHELXL-97refinement
RefinementMethod to determine structure: MULTIWAVELENGTH ANOMALOUS DIFFRACTION USING SELENOMETHIONINE (SELENIUM) AS ANOMALOUS SCATTERER
Resolution: 2→15 Å / Num. parameters: 949 / Num. restraintsaints: 862 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.3212 2950 -RANDOM
Rwork0.2377 ---
all0.2375 345321 --
obs0.2375 26629 86.9 %-
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2369
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 0 264 2369
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.023
X-RAY DIFFRACTIONs_zero_chiral_vol0.029
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.036
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.1
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.927
X-RAY DIFFRACTIONs_plane_restr0.023
X-RAY DIFFRACTIONs_chiral_restr0.036

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