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protein Protein-protein interface(s) links
Cytokine PDB id
1f2l
Jmol
Contents
Protein chains
64 a.a. *
70 a.a. *
Waters ×264
* Residue conservation analysis
PDB id:
1f2l
Name: Cytokine
Title: Crystal structure of chemokine domain of fractalkine
Structure: Fractalkine. Chain: a, b, c, d. Fragment: chemokine domain. Synonym: neurotactin, cx3c membrane-anchored chemokine, small inducible cytokine d1. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PQS)
Resolution:
2.00Å     R-factor:   0.237     R-free:   0.321
Authors: D.M.Hoover,L.S.Mizoue,T.M.Handel,J.Lubkowski
Key ref:
D.M.Hoover et al. (2000). The crystal structure of the chemokine domain of fractalkine shows a novel quaternary arrangement. J Biol Chem, 275, 23187-23193. PubMed id: 10770945 DOI: 10.1074/jbc.M002584200
Date:
26-May-00     Release date:   06-Sep-00    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P78423  (X3CL1_HUMAN) -  Fractalkine
Seq:
Struc: 		397 a.a.
64 a.a.
Protein chain
Pfam   ArchSchema ?
P78423  (X3CL1_HUMAN) -  Fractalkine
Seq:
Struc: 		397 a.a.
70 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     immune response   1 term 
  Biochemical function     chemokine activity     1 term  

 

 
DOI no: 10.1074/jbc.M002584200 J Biol Chem 275:23187-23193 (2000)
PubMed id: 10770945  
 
 
The crystal structure of the chemokine domain of fractalkine shows a novel quaternary arrangement.
D.M.Hoover, L.S.Mizoue, T.M.Handel, J.Lubkowski.
 
  ABSTRACT  
 
Fractalkine, or neurotactin, is a chemokine that is present in endothelial cells from several tissues, including brain, liver, and kidney. It is the only member of the CX(3)C class of chemokines. Fractalkine contains a chemokine domain (CDF) attached to a membrane-spanning domain via a mucin-like stalk. However, fractalkine can also be proteolytically cleaved from its membrane-spanning domain to release a freely diffusible form. Fractalkine attracts and immobilizes leukocytes by binding to its receptor, CX(3)CR1. The x-ray crystal structure of CDF has been solved and refined to 2.0 A resolution. The CDF monomers form a dimer through an intermolecular beta-sheet. This interaction is somewhat similar to that seen in other dimeric CC chemokine crystal structures. However, the displacement of the first disulfide in CDF causes the dimer to assume a more compact quaternary structure relative to CC chemokines, which is unique to CX(3)C chemokines. Although fractalkine can bind to heparin in vitro, as shown by comparison of electrostatic surface plots with other chemokines and by heparin chromatography, the role of this property in vivo is not well understood.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Stereo drawing showing the superposition of CDF monomers. The monomers are colored as in Fig. 1. The monomers were superimposed using the program ALIGN (40), with all atoms included, and the figure was made using the program MOLSCRIPT (41). 		Figure 3.
Fig. 3. Ribbon drawing of the CDF monomers. Shown here is a representation of monomer D. Monomer B is nearly identical to monomer D, whereas monomers A and D differ within residues 5-15. Also, residues 68-74 are ordered in monomer D producing a C-terminal extension of the -helix by 1.5 turns (see "Results"). This drawing was made using the program MOLSCRIPT (41).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 23187-23193) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21223963 C.L.Salanga, and T.M.Handel (2011).
Chemokine oligomerization and interactions with receptors and glycosaminoglycans: the role of structural dynamics in function.
  Exp Cell Res, 317, 590-601.  
18725411 P.Hermand, F.Pincet, S.Carvalho, H.Ansanay, E.Trinquet, M.Daoudi, C.Combadière, and P.Deterre (2008).
Functional adhesiveness of the CX3CL1 chemokine requires its aggregation. Role of the transmembrane domain.
  J Biol Chem, 283, 30225-30234.  
17151939 Y.Becker (2007).
The spreading of HIV-1 infection in the human organism is caused by fractalkine trafficking of the infected lymphocytes--a review, hypothesis and implications for treatment.
  Virus Genes, 34, 93.  
15880599 A.Inoue, H.Hasegawa, M.Kohno, M.R.Ito, M.Terada, T.Imai, O.Yoshie, M.Nose, and S.Fujita (2005).
Antagonist of fractalkine (CX3CL1) delays the initiation and ameliorates the progression of lupus nephritis in MRL/lpr mice.
  Arthritis Rheum, 52, 1522-1533.  
  12737818 G.J.Swaminathan, D.E.Holloway, R.A.Colvin, G.K.Campanella, A.C.Papageorgiou, A.D.Luster, and K.R.Acharya (2003).
Crystal structures of oligomeric forms of the IP-10/CXCL10 chemokine.
  Structure, 11, 521-532.
PDB codes: 1o7y 1o7z 1o80
11807180 E.J.Fernandez, and E.Lolis (2002).
Structure, function, and inhibition of chemokines.
  Annu Rev Pharmacol Toxicol, 42, 469-499.  
11830659 H.Lortat-Jacob, A.Grosdidier, and A.Imberty (2002).
Structural diversity of heparan sulfate binding domains in chemokines.
  Proc Natl Acad Sci U S A, 99, 1229-1234.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.