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PDBsum entry 1ifa

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Glycoprotein PDB id
1ifa
Jmol
Contents
Protein chain
158 a.a.* *
Ligands
ASN
* Residue conservation analysis
* C-alpha coords only
PDB id:
1ifa
Name: Glycoprotein
Title: Three-dimensional crystal structure of recombinant murine interferon-beta
Structure: Interferon-beta. Chain: a. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090
Resolution:
2.60Å     R-factor:   0.205    
Authors: Y.Mitsui,T.Senda,S.Matsuda,G.Kawano,K.T.Nakamura,H.Shimizu
Key ref: T.Senda et al. (1992). Three-dimensional crystal structure of recombinant murine interferon-beta. EMBO J, 11, 3193-3201. PubMed id: 1505514
Date:
29-Oct-91     Release date:   31-Jan-94    
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01575  (IFNB_MOUSE) -  Interferon beta
Seq:
Struc:
182 a.a.
158 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     cellular response to interferon-beta   24 terms 
  Biochemical function     cytokine activity     3 terms  

 

 
    Key reference    
 
 
EMBO J 11:3193-3201 (1992)
PubMed id: 1505514  
 
 
Three-dimensional crystal structure of recombinant murine interferon-beta.
T.Senda, T.Shimazu, S.Matsuda, G.Kawano, H.Shimizu, K.T.Nakamura, Y.Mitsui.
 
  ABSTRACT  
 
The crystal structure of recombinant murine interferon-beta (IFN-beta) has been solved by the multiple isomorphous replacement method and refined to an R-factor of 20.5% against 2.6 A X-ray diffraction data. The structure shows a variant of the alpha-helix bundle with a new chain-folding topology, which seems to represent a basic structural framework of all the IFN-alpha and IFN-beta molecules belonging to the type I family. Functionally important segments of the polypeptide chain, as implied through numerous gene manipulation studies carried out so far, are spatially clustered indicating the binding site(s) to the receptor(s). Comparison of the present structure with those of other alpha-helical cytokine proteins, including porcine growth hormone, interleukin 2 and interferon gamma, indicated either a topological similarity in chain folding or a similar spatial arrangement of the alpha-helices.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21367553 H.Yamaguchi, Y.Hirakura, H.Shirai, H.Mimura, and T.Toyo'oka (2011).
Quantitative evaluation of protein conformation in pharmaceuticals using cross-linking reactions coupled with LC-MS/MS analysis.
  J Pharm Biomed Anal, 55, 574-582.  
20712454 H.H.Gad, O.J.Hamming, and R.Hartmann (2010).
The structure of human interferon lambda and what it has taught us.
  J Interferon Cytokine Res, 30, 565-571.  
20047337 S.R.Akabayov, Z.Biron, P.Lamken, J.Piehler, and J.Anglister (2010).
NMR mapping of the IFNAR1-EC binding site on IFNalpha2 reveals allosteric changes in the IFNAR2-EC binding site.
  Biochemistry, 49, 687-695.  
18252254 Z.Li, J.J.Strunk, P.Lamken, J.Piehler, and T.Walz (2008).
The EM structure of a type I interferon-receptor complex reveals a novel mechanism for cytokine signaling.
  J Mol Biol, 377, 715-724.  
16734561 C.Sommereyns, and T.Michiels (2006).
N-glycosylation of murine IFN-beta in a putative receptor-binding region.
  J Interferon Cytokine Res, 26, 406-413.  
14585200 B.Robertsen, V.Bergan, T.Røkenes, R.Larsen, and A.Albuquerque (2003).
Atlantic salmon interferon genes: cloning, sequence analysis, expression, and biological activity.
  J Interferon Cytokine Res, 23, 601-612.  
14651780 D.Platis, and G.R.Foster (2003).
Activity of hybrid type I interferons in cells lacking Tyk2: a common region of IFN-alpha 8 induces a response, but IFN-alpha2/8 hybrids can behave like IFN-beta.
  J Interferon Cytokine Res, 23, 655-666.  
12915574 S.Kawamoto, K.Oritani, H.Asada, I.Takahashi, J.Ishikawa, H.Yoshida, M.Yamada, N.Ishida, H.Ujiie, H.Masaie, Y.Tomiyama, and Y.Matsuzawa (2003).
Antiviral activity of limitin against encephalomyocarditis virus, herpes simplex virus, and mouse hepatitis virus: diverse requirements by limitin and alpha interferon for interferon regulatory factor 1.
  J Virol, 77, 9622-9631.  
12021428 Y.Liu, and D.Eisenberg (2002).
3D domain swapping: as domains continue to swap.
  Protein Sci, 11, 1285-1299.  
11544103 K.Oritani, P.W.Kincade, C.Zhang, Y.Tomiyama, and Y.Matsuzawa (2001).
Type I interferons and limitin: a comparison of structures, receptors, and functions.
  Cytokine Growth Factor Rev, 12, 337-348.  
11905829 W.J.Leonard (2001).
Cytokines and immunodeficiency diseases.
  Nat Rev Immunol, 1, 200-208.  
10722045 S.Orrù, A.Amoresano, R.Siciliano, R.Napoleoni, O.Finocchiaro, A.Datola, E.De Luca, A.Sirna, and P.Pucci (2000).
Structural analysis of modified forms of recombinant IFN-beta produced under stress-simulating conditions.
  Biol Chem, 381, 7.  
9692957 J.M.Matthews, A.Hammacher, G.J.Howlett, and R.J.Simpson (1998).
Physicochemical characterization of an antagonistic human interleukin-6 dimer.
  Biochemistry, 37, 10671-10680.  
9261551 G.C.Viscomi (1997).
Structure-activity of type I interferons.
  Biotherapy, 10, 59-86.  
9288895 M.C.Olcott, and B.E.Haley (1997).
Identification of an adenine-nucleotide-binding site on interferon alpha2.
  Eur J Biochem, 247, 762-769.  
9197998 Y.Mitsui, and T.Senda (1997).
Elucidation of the basic three-dimensional structure of type I interferons and its functional and evolutionary implications.
  J Interferon Cytokine Res, 17, 319-326.  
8910760 A.Iwata, T.Saito, N.Mizukoshi-Iwata, M.Fujino, A.Katsumata, K.Hamada, Y.Sokawa, and S.Ueda (1996).
Cloning and expression of the canine interferon-beta gene.
  J Interferon Cytokine Res, 16, 765-770.  
8555185 C.Nishimura, A.Watanabe, H.Gouda, I.Shimada, and Y.Arata (1996).
Folding topologies of human interleukin-6 and its mutants as studied by NMR spectroscopy.
  Biochemistry, 35, 273-281.  
8813328 J.Langer, G.Garotta, and S.Pestka (1996).
Interferon receptors.
  Biotherapy, 8, 163-174.  
7777489 A.Gustchina, A.Zdanov, C.Schalk-Hihi, and A.Wlodawer (1995).
A model of the complex between interleukin-4 and its receptors.
  Proteins, 21, 140-148.
PDB code: 1ite
7648431 G.Uzé, G.Lutfalla, and K.E.Mogensen (1995).
Alpha and beta interferons and their receptor and their friends and relations.
  J Interferon Cytokine Res, 15, 3.  
7773741 H.R.Mott, and I.D.Campbell (1995).
Four-helix bundle growth factors and their receptors: protein-protein interactions.
  Curr Opin Struct Biol, 5, 114-121.  
7494857 M.A.Horisberger, and S.Di Marco (1995).
Interferon-alpha hybrids.
  Pharmacol Ther, 66, 507-534.  
  7613464 M.H.Seto, R.N.Harkins, M.Adler, M.Whitlow, W.B.Church, and E.Croze (1995).
Homology model of human interferon-alpha 8 and its receptor complex.
  Protein Sci, 4, 655-670.  
  8580836 M.J.Bennett, M.P.Schlunegger, and D.Eisenberg (1995).
3D domain swapping: a mechanism for oligomer assembly.
  Protein Sci, 4, 2455-2468.  
  7517984 A.P.Korn, D.R.Rose, and E.N.Fish (1994).
Three-dimensional model of a human interferon-alpha consensus sequence.
  J Interferon Res, 14, 1-9.  
8069631 D.A.Rozwarski, A.M.Gronenborn, G.M.Clore, J.F.Bazan, A.Bohm, A.Wlodawer, M.Hatada, and P.A.Karplus (1994).
Structural comparisons among the short-chain helical cytokines.
  Structure, 2, 159-173.  
8159715 M.J.Bennett, S.Choe, and D.Eisenberg (1994).
Domain swapping: entangling alliances between proteins.
  Proc Natl Acad Sci U S A, 91, 3127-3131.  
  7521382 M.J.Sekellick, A.F.Ferrandino, D.A.Hopkins, and P.I.Marcus (1994).
Chicken interferon gene: cloning, expression, and analysis.
  J Interferon Res, 14, 71-79.  
  7511100 R.Savino, A.Lahm, A.L.Salvati, L.Ciapponi, E.Sporeno, S.Altamura, G.Paonessa, C.Toniatti, and G.Ciliberto (1994).
Generation of interleukin-6 receptor antagonists by molecular-modeling guided mutagenesis of residues important for gp130 activation.
  EMBO J, 13, 1357-1367.  
  7881359 S.Lok, and D.C.Foster (1994).
The structure, biology and potential therapeutic applications of recombinant thrombopoietin.
  Stem Cells, 12, 586-598.  
  8401223 A.Wlodawer, A.Pavlovsky, and A.Gustchina (1993).
Hematopoietic cytokines: similarities and differences in the structures, with implications for receptor binding.
  Protein Sci, 2, 1373-1382.  
  8253075 C.M.Owczarek, M.J.Layton, D.Metcalf, P.Lock, T.A.Willson, N.M.Gough, and N.A.Nicola (1993).
Inter-species chimeras of leukaemia inhibitory factor define a major human receptor-binding determinant.
  EMBO J, 12, 3487-3495.  
7685117 C.P.Hill, T.D.Osslund, and D.Eisenberg (1993).
The structure of granulocyte-colony-stimulating factor and its relationship to other growth factors.
  Proc Natl Acad Sci U S A, 90, 5167-5171.
PDB code: 1rhg
8234245 N.J.Murgolo, W.T.Windsor, A.Hruza, P.Reichert, A.Tsarbopoulos, S.Baldwin, E.Huang, B.Pramanik, S.Ealick, and P.P.Trotta (1993).
A homology model of human interferon alpha-2.
  Proteins, 17, 62-74.
PDB codes: 2hie 2hif
8223648 T.Voss, E.Ergülen, H.Ahorn, V.Kubelka, K.Sugiyama, I.Maurer-Fogy, and J.Glössl (1993).
Expression of human interferon omega 1 in Sf9 cells. No evidence for complex-type N-linked glycosylation or sialylation.
  Eur J Biochem, 217, 913-919.  
8415875 Y.Mitsui, T.Senda, T.Shimazu, S.Matsuda, and J.Utsumi (1993).
Structural, functional and evolutionary implications of the three-dimensional crystal structure of murine interferon-beta.
  Pharmacol Ther, 58, 93.  
1483478 M.Vincent, I.M.Li De La Sierra, M.N.Berberan-Santos, A.Diaz, M.Diaz, G.Padron, and J.Gallay (1992).
Time-resolved fluorescence study of human recombinant interferon alpha 2. Association state of the protein, spatial proximity of the two tryptophan residues.
  Eur J Biochem, 210, 953-961.  
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 code is shown on the right.