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PDBsum entry 1iob

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protein links
Cytokine PDB id
1iob
Jmol
Contents
Protein chain
153 a.a. *
Waters ×7
* Residue conservation analysis
PDB id:
1iob
Name: Cytokine
Title: Interleukin-1 beta from joint x-ray and nmr refinement
Structure: Interleukin-1 beta. Chain: a. Synonym: catabolin
Source: Homo sapiens. Human. Organism_taxid: 9606
Resolution:
2.00Å     R-factor:   0.214     R-free:   0.254
Authors: B.Shaanan,G.M.Clore
Key ref: B.Shaanan et al. (1992). Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement. Science, 257, 961-964. PubMed id: 1502561 DOI: 10.1126/science.1502561
Date:
14-Mar-96     Release date:   17-Aug-96    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01584  (IL1B_HUMAN) -  Interleukin-1 beta
Seq:
Struc:
269 a.a.
153 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     immune response   2 terms 
  Biochemical function     receptor binding     2 terms  

 

 
DOI no: 10.1126/science.1502561 Science 257:961-964 (1992)
PubMed id: 1502561  
 
 
Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement.
B.Shaanan, A.M.Gronenborn, G.H.Cohen, G.L.Gilliland, B.Veerapandian, D.R.Davies, G.M.Clore.
 
  ABSTRACT  
 
Joint refinement of macromolecules against crystallographic and nuclear magnetic resonance (NMR) observations is presented as a way of combining experimental information from the two methods. The model of interleukin-1 beta derived by the joint x-ray and NMR refinement is shown to be consistent with the experimental observations of both methods and to have crystallographic R value and geometrical parameters that are of the same quality as or better than those of models obtained by conventional crystallographic studies. The few NMR observations that are violated by the model serve as an indicator for genuine differences between the crystal and solution structures. The joint x-ray-NMR refinement can resolve structural ambiguities encountered in studies of multidomain proteins, in which low- to medium-resolution diffraction data can be complemented by higher resolution NMR data obtained for the individual domains.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19597943 L.Shi, N.J.Traaseth, R.Verardi, A.Cembran, J.Gao, and G.Veglia (2009).
A refinement protocol to determine structure, topology, and depth of insertion of membrane proteins using hybrid solution and solid-state NMR restraints.
  J Biomol NMR, 44, 195-205.  
18816799 T.A.Ramelot, S.Raman, A.P.Kuzin, R.Xiao, L.C.Ma, T.B.Acton, J.F.Hunt, G.T.Montelione, D.Baker, and M.A.Kennedy (2009).
Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study.
  Proteins, 75, 147-167.
PDB codes: 1tvg 1xpw
17340198 G.Vergoten, and J.P.Zanetta (2007).
Structural differences between the putative carbohydrate-recognition domains of human IL-1 alpha, IL-1 beta and IL-1 receptor antagonist obtained by in silico modeling.
  Glycoconj J, 24, 183-193.  
16800891 K.Brunner, W.Gronwald, J.M.Trenner, K.P.Neidig, and H.R.Kalbitzer (2006).
A general method for the unbiased improvement of solution NMR structures by the use of related X-ray data, the AUREMOL-ISIC algorithm.
  BMC Struct Biol, 6, 14.  
15371276 Y.Iwamoto, T.Kaneko, J.Ichinose, T.Mōri, Y.Shibata, K.Toshimori, and H.Iida (2005).
Molecular cloning of rat Spetex2 family genes mapped on chromosome 15p16, encoding a 23-kilodalton protein associated with the plasma membranes of haploid spermatids.
  Biol Reprod, 72, 284-292.  
15236321 H.Iida, J.Ichinose, T.Kaneko, T.Mōri, and Y.Shibata (2004).
Complementary DNA cloning of rat spetex-1, a spermatid-expressing gene-1, encoding a 63 kDa cytoplasmic protein of elongate spermatids.
  Mol Reprod Dev, 68, 385-393.  
12646494 H.Iida, A.Urasoko, M.Doiguchi, T.Mōri, K.Toshimori, and Y.Shibata (2003).
Complementary DNA cloning and characterization of rat spergen-2, a spermatogenic cell-specific gene 2 encoding a 56-kilodalton nuclear protein bearing ankyrin repeat motifs.
  Biol Reprod, 69, 421-429.  
12554939 M.G.Rudolph, M.S.Kelker, T.R.Schneider, T.O.Yeates, V.Oseroff, D.K.Heidary, P.A.Jennings, and I.A.Wilson (2003).
Use of multiple anomalous dispersion to phase highly merohedrally twinned crystals of interleukin-1beta.
  Acta Crystallogr D Biol Crystallogr, 59, 290-298.
PDB code: 1l2h
8968609 B.S.Chang, R.M.Beauvais, T.Arakawa, L.O.Narhi, A.Dong, D.I.Aparisio, and J.F.Carpenter (1996).
Formation of an active dimer during storage of interleukin-1 receptor antagonist in aqueous solution.
  Biophys J, 71, 3399-3406.  
7984623 A.M.Gronenborn, and G.M.Clore (1994).
Where is NMR taking us?
  Proteins, 19, 273-276.  
7664036 L.J.Smith, C.Redfield, R.A.Smith, C.M.Dobson, G.M.Clore, A.M.Gronenborn, M.R.Walter, T.L.Naganbushan, and A.Wlodawer (1994).
Comparison of four independently determined structures of human recombinant interleukin-4.
  Nat Struct Biol, 1, 301-310.  
  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.  
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.