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PDBsum entry 2i1b

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protein links
Cytokine PDB id
2i1b
Jmol
Contents
Protein chain
153 a.a. *
Waters ×168
* Residue conservation analysis
PDB id:
2i1b
Name: Cytokine
Title: Crystallographic refinement of interleukin-1 beta at 2.0 angstroms resolution
Structure: Interleukin-1 beta. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.00Å     R-factor:   0.172    
Authors: J.P.Priestle,H.-P.Schaer,M.G.Gruetter
Key ref: J.P.Priestle et al. (1989). Crystallographic refinement of interleukin 1 beta at 2.0 A resolution. Proc Natl Acad Sci U S A, 86, 9667-9671. PubMed id: 2602367 DOI: 10.1073/pnas.86.24.9667
Date:
02-Jan-90     Release date:   15-Apr-90    
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

 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: 10.1073/pnas.86.24.9667 Proc Natl Acad Sci U S A 86:9667-9671 (1989)
PubMed id: 2602367  
 
 
Crystallographic refinement of interleukin 1 beta at 2.0 A resolution.
J.P.Priestle, H.P.Schär, M.G.Grütter.
 
  ABSTRACT  
 
The structure of human recombinant interleukin 1 beta (IL-1 beta) has been refined by a restrained least-squares method to a crystallographic R factor of 17.2% to 2.0 A resolution. One-hundred sixty-eight solvent molecules have been located, and isotropic temperature factors for each atom have been refined. The overall structure is composed of 12 beta-strands that can best be described as forming the four triangular faces of a tetrahedron with hydrogen bonding resembling normal antiparallel beta-sheets only at the vertices. The interior of this tetrahedron is filled by hydrophobic side chains. Analysis of sequence alignments with IL-1 beta from other mammalian species shows the interior to be very well conserved with the exterior residues markedly less so. There does not appear to be a clustering of invariant amino acid side chains on the surface of the molecule, suggesting an area of interaction with the IL-1 receptor. Comparison of the IL-1 beta structure with IL-1 alpha sequences indicates that IL-1 alpha probably has a similar overall folding as IL-1 beta but binds to the receptor in a different fashion. The three-dimensional structure of the IL-1 beta is analyzed in light of what has been suggested by previously published work on mutants and fragments of the molecule.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20177398 C.Gabay, C.Lamacchia, and G.Palmer (2010).
IL-1 pathways in inflammation and human diseases.
  Nat Rev Rheumatol, 6, 232-241.  
20802483 D.Wang, S.Zhang, L.Li, X.Liu, K.Mei, and X.Wang (2010).
Structural insights into the assembly and activation of IL-1β with its receptors.
  Nat Immunol, 11, 905-911.
PDB code: 3o4o
20935647 M.F.Nold, C.A.Nold-Petry, J.A.Zepp, B.E.Palmer, P.Bufler, and C.A.Dinarello (2010).
IL-37 is a fundamental inhibitor of innate immunity.
  Nat Immunol, 11, 1014-1022.  
19836339 A.Lingel, T.M.Weiss, M.Niebuhr, B.Pan, B.A.Appleton, C.Wiesmann, J.F.Bazan, and W.J.Fairbrother (2009).
Structure of IL-33 and its interaction with the ST2 and IL-1RAcP receptors--insight into heterotrimeric IL-1 signaling complexes.
  Structure, 17, 1398-1410.
PDB code: 2kll
  19241368 B.W.Matthews, and L.Liu (2009).
A review about nothing: are apolar cavities in proteins really empty?
  Protein Sci, 18, 494-502.  
19776018 I.C.Wilkinson, C.J.Hall, V.Veverka, J.Y.Shi, F.W.Muskett, P.E.Stephens, R.J.Taylor, A.J.Henry, and M.D.Carr (2009).
High resolution NMR-based model for the structure of a scFv-IL-1beta complex: potential for NMR as a key tool in therapeutic antibody design and development.
  J Biol Chem, 284, 31928-31935.
PDB code: 2kh2
19805131 J.A.Vila, Y.A.Arnautova, O.A.Martin, and H.A.Scheraga (2009).
Quantum-mechanics-derived 13Calpha chemical shift server (CheShift) for protein structure validation.
  Proc Natl Acad Sci U S A, 106, 16972-16977.  
18827826 R.Kakkar, and R.T.Lee (2008).
The IL-33/ST2 pathway: therapeutic target and novel biomarker.
  Nat Rev Drug Discov, 7, 827-840.  
  17277441 N.Kulahin, V.Kiselyov, A.Kochoyan, O.Kristensen, J.S.Kastrup, V.Berezin, E.Bock, and M.Gajhede (2007).
Structure of rat acidic fibroblast growth factor at 1.4 A resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 65-68.
PDB code: 2j3p
17131430 V.Helms (2007).
Protein dynamics tightly connected to the dynamics of surrounding and internal water molecules.
  Chemphyschem, 8, 23-33.  
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
15382229 M.J.Bernett, T.Somasundaram, and M.Blaber (2004).
An atomic resolution structure for human fibroblast growth factor 1.
  Proteins, 57, 626-634.
PDB code: 1rg8
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
14627732 S.R.Brych, J.Kim, T.M.Logan, and M.Blaber (2003).
Accommodation of a highly symmetric core within a symmetric protein superfold.
  Protein Sci, 12, 2704-2718.
PDB codes: 1jy0 1m16 1nzk 1p63
11847289 C.Liu, J.A.Gaspar, H.J.Wong, and E.M.Meiering (2002).
Conserved and nonconserved features of the folding pathway of hisactophilin, a beta-trefoil protein.
  Protein Sci, 11, 669-679.  
11835510 D.Vitkup, D.Ringe, M.Karplus, and G.A.Petsko (2002).
Why protein R-factors are so large: a self-consistent analysis.
  Proteins, 46, 345-354.  
11714927 S.R.Brych, S.I.Blaber, T.M.Logan, and M.Blaber (2001).
Structure and stability effects of mutations designed to increase the primary sequence symmetry within the core region of a beta-trefoil.
  Protein Sci, 10, 2587-2599.
PDB codes: 1jqz 1jt3 1jt4 1jt5 1jt7 1jtc
10852706 B.A.Chrunyk, M.H.Rosner, Y.Cong, A.S.McColl, I.G.Otterness, and G.O.Daumy (2000).
Inhibiting protein-protein interactions: a model for antagonist design.
  Biochemistry, 39, 7092-7099.  
9874779 B.Yu, M.Blaber, A.M.Gronenborn, G.M.Clore, and D.L.Caspar (1999).
Disordered water within a hydrophobic protein cavity visualized by x-ray crystallography.
  Proc Natl Acad Sci U S A, 96, 103-108.
PDB code: 9ilb
10328267 J.K.Dattagupta, A.Podder, C.Chakrabarti, U.Sen, D.Mukhopadhyay, S.K.Dutta, and M.Singh (1999).
Refined crystal structure (2.3 A) of a double-headed winged bean alpha-chymotrypsin inhibitor and location of its second reactive site.
  Proteins, 35, 321-331.
PDB code: 2wbc
10531477 S.Ravichandran, U.Sen, C.Chakrabarti, and J.K.Dattagupta (1999).
Cryocrystallography of a Kunitz-type serine protease inhibitor: the 90 K structure of winged bean chymotrypsin inhibitor (WCI) at 2.13 A resolution.
  Acta Crystallogr D Biol Crystallogr, 55, 1814-1821.
PDB code: 4wbc
  9646173 C.A.Dinarello (1998).
Interleukin-1, interleukin-1 receptors and interleukin-1 receptor antagonist.
  Int Rev Immunol, 16, 457-499.  
  9286985 Y.R.Thorstenson, Y.Zhang, P.S.Olson, and D.Mascarenhas (1997).
Leaderless polypeptides efficiently extracted from whole cells by osmotic shock.
  J Bacteriol, 179, 5333-5339.  
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.  
8681939 D.C.Ambrosetti, E.Palla, A.Mirtella, C.Galeotti, E.Solito, P.Navarra, L.Parente, and M.Melli (1996).
Synthetic alleles at position 121 define a functional domain of human interleukin-1 beta.
  Eur J Biochem, 238, 308-316.  
8610159 Y.Kato, T.Muto, T.Tomura, H.Tsumura, H.Watarai, T.Mikayama, K.Ishizaka, and R.Kuroki (1996).
The crystal structure of human glycosylation-inhibiting factor is a trimeric barrel with three 6-stranded beta-sheets.
  Proc Natl Acad Sci U S A, 93, 3007-3010.
PDB code: 1gif
7867645 H.A.Schreuder, J.M.Rondeau, C.Tardif, A.Soffientini, E.Sarubbi, A.Akeson, T.L.Bowlin, S.Yanofsky, and R.W.Barrett (1995).
Refined crystal structure of the interleukin-1 receptor antagonist. Presence of a disulfide link and a cis-proline.
  Eur J Biochem, 227, 838-847.
PDB code: 1ilr
7589081 M.Svenson, S.Nedergaard, P.M.Heegaard, T.D.Whisenand, W.P.Arend, and K.Bendtzen (1995).
Differential binding of human interleukin-1 (IL-1) receptor antagonist to natural and recombinant soluble and cellular IL-1 type I receptors.
  Eur J Immunol, 25, 2842-2850.  
7919431 C.A.Dinarello (1994).
Blocking interleukin-1 receptors.
  Int J Clin Lab Res, 24, 61-79.  
8064334 J.M.Parker, and R.S.Hodges (1994).
HomologyPlot: searching for homology to a family of proteins using a database of unique conserved patterns.
  J Comput Aided Mol Des, 8, 193-210.  
  7691311 A.E.Eriksson, L.S.Cousens, and B.W.Matthews (1993).
Refinement of the structure of human basic fibroblast growth factor at 1.6 A resolution and analysis of presumed heparin binding sites by selenate substitution.
  Protein Sci, 2, 1274-1284.
PDB codes: 1fga 4fgf
8436117 F.Guinet, J.D.Guitton, N.Gault, F.Folliard, N.Touchet, J.M.Cherel, A.Crespo, A.Destourbe, P.Bertrand, and P.Denefle (1993).
Interleukin-1 beta-specific partial agonists defined by site-directed mutagenesis studies.
  Eur J Biochem, 211, 583-590.  
  8518735 J.E.Wampler, E.A.Bradley, D.E.Stewart, and M.W.Adams (1993).
Modeling the structure of Pyrococcus furiosus rubredoxin by homology to other X-ray structures.
  Protein Sci, 2, 640-649.  
1553379 B.Veerapandian, G.L.Gilliland, R.Raag, A.L.Svensson, Y.Masui, Y.Hirai, and T.L.Poulos (1992).
Functional implications of interleukin-1 beta based on the three-dimensional structure.
  Proteins, 12, 10-23.
PDB code: 4i1b
1534698 B.Veerapandian (1992).
Structure and function of interleukin-1, based on crystallographic and modeling studies.
  Biophys J, 62, 112-115.
PDB codes: 1ita 1itn
1553380 E.A.Stura, P.Chen, C.M.Wilmot, J.H.Arevalo, and I.A.Wilson (1992).
Crystallization studies of glycosylated and unglycosylated human recombinant interleukin-2.
  Proteins, 12, 24-30.  
1470680 M.Billeter (1992).
Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals.
  Q Rev Biophys, 25, 325-377.  
1528078 M.D.Walkinshaw (1992).
Protein targets for structure-based drug design.
  Med Res Rev, 12, 317-372.  
  1505514 T.Senda, T.Shimazu, S.Matsuda, G.Kawano, H.Shimizu, K.T.Nakamura, and Y.Mitsui (1992).
Three-dimensional crystal structure of recombinant murine interferon-beta.
  EMBO J, 11, 3193-3201.
PDB code: 1ifa
1707542 A.E.Eriksson, L.S.Cousens, L.H.Weaver, and B.W.Matthews (1991).
Three-dimensional structure of human basic fibroblast growth factor.
  Proc Natl Acad Sci U S A, 88, 3441-3445.  
1837145 E.Labriola-Tompkins, C.Chandran, K.L.Kaffka, D.Biondi, B.J.Graves, M.Hatada, V.S.Madison, J.Karas, P.L.Kilian, and G.Ju (1991).
Identification of the discontinuous binding site in human interleukin 1 beta for the type I interleukin 1 receptor.
  Proc Natl Acad Sci U S A, 88, 11182-11186.  
1826365 G.Ju, E.Labriola-Tompkins, C.A.Campen, W.R.Benjamin, J.Karas, J.Plocinski, D.Biondi, K.L.Kaffka, P.L.Kilian, and S.P.Eisenberg (1991).
Conversion of the interleukin 1 receptor antagonist into an agonist by site-specific mutagenesis.
  Proc Natl Acad Sci U S A, 88, 2658-2662.  
1849658 J.D.Zhang, L.S.Cousens, P.J.Barr, and S.R.Sprang (1991).
Three-dimensional structure of human basic fibroblast growth factor, a structural homolog of interleukin 1 beta.
  Proc Natl Acad Sci U S A, 88, 3446-3450.
PDB code: 2fgf
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.