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PDBsum entry 1s0l

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Immune response PDB id
1s0l
Jmol
Contents
Protein chain
153 a.a. *
Waters ×77
* Residue conservation analysis
PDB id:
1s0l
Name: Immune response
Title: Interleukin 1 beta mutant f42w
Structure: Interleukin-1 beta. Chain: a. Fragment: interleukin 1-b. Synonym: il-1 beta, catabolin. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: il1b. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.34Å     R-factor:   0.191     R-free:   0.222
Authors: D.H.Adamek,L.Guerrero,D.L.D.Caspar
Key ref:
D.H.Adamek et al. (2005). Structural and energetic consequences of mutations in a solvated hydrophobic cavity. J Mol Biol, 346, 307-318. PubMed id: 15663946 DOI: 10.1016/j.jmb.2004.11.046
Date:
31-Dec-03     Release date:   30-Mar-04    
PROCHECK
Go to PROCHECK summary
 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
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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: 10.1016/j.jmb.2004.11.046 J Mol Biol 346:307-318 (2005)
PubMed id: 15663946  
 
 
Structural and energetic consequences of mutations in a solvated hydrophobic cavity.
D.H.Adamek, L.Guerrero, M.Blaber, D.L.Caspar.
 
  ABSTRACT  
 
The structural and energetic consequences of modifications to the hydrophobic cavity of interleukin 1-beta (IL-1beta) are described. Previous reports demonstrated that the entirely hydrophobic cavity of IL-1beta contains positionally disordered water. To gain a better understanding of the nature of this cavity and the water therein, a number of mutant proteins were constructed by site-directed mutagenesis, designed to result in altered hydrophobicity of the cavity. These mutations involve the replacement of specific phenylalanine residues, which circumscribe the cavity, with tyrosine, tryptophan, leucine and isoleucine. Using differential scanning calorimetry to determine the relative stabilities of the wild-type and mutant proteins, we found all of the mutants to be destabilizing. X-ray crystallography was used to identify the structural consequences of the mutations. No clear correlation between the hydrophobicities of the specific side-chains introduced and the resulting stabilities was found.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Ball and stick diagram of the cavity residues of wild-type Il-1b. The wire contour represents positionally disordered water observed crystallographically. The triad of phenylalanine residues that circumscribe the cavity are shown in gray. Phenylalanine 101 (dark gray) is not solvent-accessible from the cavity. All other residues shown in light grey are the residues that form the cavity. Image adapted from Yu et al.2
Figure 5.
Figure 5. Local structure of F101Y around the mutation site. The stereograph ball and stick model of the mutant structure is shown superposed over the darker, smaller, wild-type structure. Large dark spheres represent water molecules. Dotted lines represent putative hydrogen bonds.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 346, 307-318) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21290601 J.V.Jokerst, J.Chou, J.P.Camp, J.Wong, A.Lennart, A.A.Pollard, P.N.Floriano, N.Christodoulides, G.W.Simmons, Y.Zhou, M.F.Ali, and J.T.McDevitt (2011).
Location of Biomarkers and Reagents within Agarose Beads of a Programmable Bio-nano-chip.
  Small, 7, 613-624.  
20665475 M.Bueno, N.A.Temiz, and C.J.Camacho (2010).
Novel modulation factor quantifies the role of water molecules in protein interactions.
  Proteins, 78, 3226-3234.  
17380484 S.Somani, C.P.Chng, and C.S.Verma (2007).
Hydration of a hydrophobic cavity and its functional role: a simulation study of human interleukin-1beta.
  Proteins, 67, 868-885.  
16877708 M.Bueno, L.A.Campos, J.Estrada, and J.Sancho (2006).
Energetics of aliphatic deletions in protein cores.
  Protein Sci, 15, 1858-1872.  
17179045 M.L.Quillin, P.T.Wingfield, and B.W.Matthews (2006).
Determination of solvent content in cavities in IL-1beta using experimentally phased electron density.
  Proc Natl Acad Sci U S A, 103, 19749-19753.
PDB code: 2nvh
17038664 P.Cioni (2006).
Role of protein cavities on unfolding volume change and on internal dynamics under pressure.
  Biophys J, 91, 3390-3396.  
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.