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PDBsum entry 1ijz

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protein links
Cytokine PDB id
1ijz
Jmol
Contents
Protein chain
113 a.a. *
* Residue conservation analysis
PDB id:
1ijz
Name: Cytokine
Title: Solution structure of human il-13
Structure: Interleukin-13. Chain: a. Synonym: il-13. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 1 models
Authors: F.J.Moy,E.Diblasio,J.Wilhelm,R.Powers
Key ref:
F.J.Moy et al. (2001). Solution structure of human IL-13 and implication for receptor binding. J Mol Biol, 310, 219-230. PubMed id: 11419948 DOI: 10.1006/jmbi.2001.4764
Date:
01-May-01     Release date:   01-May-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P35225  (IL13_HUMAN) -  Interleukin-13
Seq:
Struc:
146 a.a.
113 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   4 terms 
  Biological process     cellular response to mechanical stimulus   28 terms 
  Biochemical function     protein binding     4 terms  

 

 
DOI no: 10.1006/jmbi.2001.4764 J Mol Biol 310:219-230 (2001)
PubMed id: 11419948  
 
 
Solution structure of human IL-13 and implication for receptor binding.
F.J.Moy, E.Diblasio, J.Wilhelm, R.Powers.
 
  ABSTRACT  
 
Interleukin-13 has been implicated as a key factor in asthma, allergy, atopy and inflammatory response, establishing the protein as a valuable therapeutic target. The high-resolution solution structure of human IL-13 has been determined by multidimensional NMR. The resulting structure is consistent with previous short-chain left-handed four-helix bundles, where a significant similarity in the folding topology between IL-13 and IL-4 was observed. IL-13 shares a significant overlap in biological function with IL-4, a result of the common alpha chain component (IL-4Ralpha) in their respective receptors. Based on the available structural and mutational data, an IL-13/IL-4Ralpha model and a sequential mechanism for forming the signaling heterodimer is proposed for IL-13.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. (a) and (c) GRASP molecular surface of the IL-4 and IL-13 NMR structures, respectively, where residues identified from mutational analysis that correlate with IL-4Ra affinity are colored blue. Residues proposed to interact with either the g[C] or IL-13 binding chain (BC) are colored red. Residues in the IL-4Ra binding sites that were mutated are labeled. (b) and (d) The same molecular surface and view for the IL-4 and IL-13 structures, respectively, colored by electrostatic potential, where red corresponds to negative, blue to positive and white to neutral.
Figure 7.
Figure 7. (a) IL-13/IL-4Ra model based on the IL-4/IL-4Ra X-ray structure (PDB ID:1IRA)[18]. IL-13 replaced IL-4 in the IL-4/IL-4Ra X-ray structure by overlaying IL-13 onto IL-4 based on the common secondary structure elements and cysteine residues (see Figure 4). IL-4Ra is shown as a molecular surface (green) and IL-13 as a ribbon diagram colored by secondary structure, where the helices are colored purple and the b-sheets are colored yellow. Only the IL-13/IL-4Ra interface is illustrated. The secondary structure elements are labeled. (b) Expanded view of the IL-13/IL-4Ra binding site indicating the interaction with helix a[A] from IL-13. (c) Expanded view of the IL-13/IL-4Ra binding site illustrating the interaction with helix a[C] from IL-13. The side-chains for critical residues based on the IL-4/IL-4Ra X-ray structure and mutational data are shown and labeled. Residues from IL-4Ra are labeled with the prefix r. The side-chains are colored by element type, the backbone atoms for IL-13 and IL-4Ra are colored magenta and blue, respectively.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 310, 219-230) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21377040 M.Akdis, S.Burgler, R.Crameri, T.Eiwegger, H.Fujita, E.Gomez, S.Klunker, N.Meyer, L.O'Mahony, O.Palomares, C.Rhyner, N.Quaked, A.Schaffartzik, W.Van De Veen, S.Zeller, M.Zimmermann, and C.A.Akdis (2011).
Interleukins, from 1 to 37, and interferon-γ: receptors, functions, and roles in diseases.
  J Allergy Clin Immunol, 127, 701.  
19463093 A.N.Nekrasov, L.E.Petrovskaya, V.A.Toporova, E.A.Kryukova, A.V.Rodina, E.Y.Moskaleva, and M.P.Kirpichnikov (2009).
Design of a novel interleukin-13 antagonist from analysis of informational structure.
  Biochemistry (Mosc), 74, 399-405.  
19105661 F.O.Martinez, L.Helming, and S.Gordon (2009).
Alternative activation of macrophages: an immunologic functional perspective.
  Annu Rev Immunol, 27, 451-483.  
18560827 M.Ohtani, N.Hayashi, K.Hashimoto, T.Nakanishi, and J.M.Dijkstra (2008).
Comprehensive clarification of two paralogous interleukin 4/13 loci in teleost fish.
  Immunogenetics, 60, 383-397.  
18243101 S.L.LaPorte, Z.S.Juo, J.Vaclavikova, L.A.Colf, X.Qi, N.M.Heller, A.D.Keegan, and K.C.Garcia (2008).
Molecular and structural basis of cytokine receptor pleiotropy in the interleukin-4/13 system.
  Cell, 132, 259-272.
PDB codes: 3bpl 3bpn 3bpo
16640778 M.Kraich, M.Klein, E.Patiño, H.Harrer, J.Nickel, W.Sebald, and T.D.Mueller (2006).
A modular interface of IL-4 allows for scalable affinity without affecting specificity for the IL-4 receptor.
  BMC Biol, 4, 13.
PDB codes: 2b8u 2b8x 2b8y 2b8z 2b90 2b91 2d48
16374783 Y.J.Huang, R.Tejero, R.Powers, and G.T.Montelione (2006).
A topology-constrained distance network algorithm for protein structure determination from NOESY data.
  Proteins, 62, 587-603.  
  15711639 F.D.Vladich, S.M.Brazille, D.Stern, M.L.Peck, R.Ghittoni, and D.Vercelli (2005).
IL-13 R130Q, a common variant associated with allergy and asthma, enhances effector mechanisms essential for human allergic inflammation.
  J Clin Invest, 115, 747-754.  
15870068 K.Arima, K.Sato, G.Tanaka, S.Kanaji, T.Terada, E.Honjo, R.Kuroki, Y.Matsuo, and K.Izuhara (2005).
Characterization of the interaction between interleukin-13 and interleukin-13 receptors.
  J Biol Chem, 280, 24915-24922.  
  15068667 A.B.Madhankumar, A.Mintz, and W.Debinski (2004).
Interleukin 13 mutants of enhanced avidity toward the glioma-associated receptor, IL13Ralpha2.
  Neoplasia, 6, 15-22.  
14674938 A.P.Knutsen, P.S.Hutchinson, G.M.Albers, J.Consolino, J.Smick, and V.P.Kurup (2004).
Increased sensitivity to IL-4 in cystic fibrosis patients with allergic bronchopulmonary aspergillosis.
  Allergy, 59, 81-87.  
12189139 A.B.Madhankumar, A.Mintz, and W.Debinski (2002).
Alanine-scanning mutagenesis of alpha-helix D segment of interleukin-13 reveals new functionally important residues of the cytokine.
  J Biol Chem, 277, 43194-43205.  
12582321 D.Vercelli (2002).
Genetics of IL-13 and functional relevance of IL-13 variants.
  Curr Opin Allergy Clin Immunol, 2, 389-393.  
12486820 L.A.Lieberman, and C.A.Hunter (2002).
The role of cytokines and their signaling pathways in the regulation of immunity to Toxoplasma gondii.
  Int Rev Immunol, 21, 373-403.  
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.