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Cytokine PDB id
1i1b
Jmol
Contents
Protein chain
151 a.a. *
Waters ×83
* Residue conservation analysis
PDB id:
1i1b
Name: Cytokine
Title: Crystal structure of recombinant human interleukin-1beta at 2.0 angstroms resolution
Structure: Interleukin-1 beta. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Cell: sk-hep-1 hematoma cells. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.00Å     R-factor:   0.189    
Authors: B.C.Finzel,K.D.Watenpaugh,H.M.Einspahr
Key ref: B.C.Finzel et al. (1989). Crystal structure of recombinant human interleukin-1 beta at 2.0 A resolution. J Mol Biol, 209, 779-791. PubMed id: 2585509 DOI: 10.1016/0022-2836(89)90606-2
Date:
05-Dec-89     Release date:   15-Jan-90    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01584  (IL1B_HUMAN) -  Interleukin-1 beta
Seq:
Struc: 		269 a.a.
151 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     growth factor activity     2 terms  

 

 
DOI no: 10.1016/0022-2836(89)90606-2 J Mol Biol 209:779-791 (1989)
PubMed id: 2585509  
 
 
Crystal structure of recombinant human interleukin-1 beta at 2.0 A resolution.
B.C.Finzel, L.L.Clancy, D.R.Holland, S.W.Muchmore, K.D.Watenpaugh, H.M.Einspahr.
 
  ABSTRACT  
 
The crystal structure of recombinant human interleukin-1 beta (IL-1 beta) has been determined at 2.0 A resolution and refined to a crystallographic R-factor of 0.19. Three heavy-atom derivatives were identified and used for multiple isomorphous replacement phasing. Interpretation of the resulting electron density map revealed a structure in which there are 12 antiparallel beta-strands and no alpha-helix. The single 153-residue polypeptide chain is folded into a six-stranded beta-barrel similar in architecture to the Kunitz-type trypsin inhibitor found in soybeans. The molecule displays approximate 3-fold symmetry about the axis of the beta-barrel. Each successive pair of component strands of the barrel brackets an extensive sequence outside the barrel that includes an additional pair of beta-strands and a prominent loop. Together, these three external segments conceal much of the perimeter and one end of the barrel, leaving only the end supporting the chain termini fully exposed. The structure can be used to identify portions of the polypeptide chain that are exposed on the surface of the molecule, some of which must be epitopes recognized by interleukin-1 beta receptors.
 

Literature references that cite this PDB file's key reference

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PDB codes: 3c9z 3ca0 3ca1 3ca3 3ca4 3ca5 3ca6 3cah
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Determination of solvent content in cavities in IL-1beta using experimentally phased electron density.
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PDB code: 2nvh
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).
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PDB code: 1l2h
12794857 N.Lozovaya, and A.D.Miller (2003).
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PDB codes: 1dqg 1dqo
10328267 J.K.Dattagupta, A.Podder, C.Chakrabarti, U.Sen, D.Mukhopadhyay, S.K.Dutta, and M.Singh (1999).
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PDB code: 2wbc
10531477 S.Ravichandran, U.Sen, C.Chakrabarti, and J.K.Dattagupta (1999).
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PDB code: 4wbc
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Structure of benzyl T-antigen disaccharide bound to Amaranthus caudatus agglutinin.
  Nat Struct Biol, 4, 779-783.
PDB codes: 1jlx 1jly
8968609 B.S.Chang, R.M.Beauvais, T.Arakawa, L.O.Narhi, A.Dong, D.I.Aparisio, and J.F.Carpenter (1996).
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Synthetic alleles at position 121 define a functional domain of human interleukin-1 beta.
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Hydrophilicity of cavities in proteins.
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8652550 M.Blaber, J.DiSalvo, and K.A.Thomas (1996).
X-ray crystal structure of human acidic fibroblast growth factor.
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PDB codes: 1afg 2afg
9007689 Y.Iwata, A.Kasuya, and S.Miyamoto (1996).
Reconstruction of the 3D coordinates of alpha-carbon atoms of proteins from a pair of stereographic figures.
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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).
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PDB code: 1ilr
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A procedure for the automatic determination of hydrophobic cores in protein structures.
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Mutations and off-pathway aggregation of proteins.
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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).
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Structural, functional and evolutionary implications of the three-dimensional crystal structure of murine interferon-beta.
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1466764 A.W.Yem, D.M.Guido, W.R.Mathews, N.D.Staite, K.A.Richard, M.D.Prairie, W.C.Krueger, D.E.Epps, and M.R.Deibel (1992).
Chemical modification of interleukin-1 beta: biochemical characterization of a carbodiimide-catalyzed intramolecular cross-linked protein.
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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.
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1470680 M.Billeter (1992).
Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals.
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1528078 M.D.Walkinshaw (1992).
Protein targets for structure-based drug design.
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1388674 P.Manavalan, D.L.Swope, and R.M.Withy (1992).
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  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.  
  2060653 A.V.Efimov (1991).
Structure of coiled beta-beta-hairpins and beta-beta-corners.
  FEBS Lett, 284, 288-292.  
1781888 C.S.Wu, S.A.Thompson, and J.T.Yang (1991).
Basic fibroblast growth factor is a beta-rich protein.
  J Protein Chem, 10, 427-436.  
1810348 D.A.Parry, E.Minasian, and S.J.Leach (1991).
Cytokine conformations: predictive studies.
  J Mol Recognit, 4, 63-75.  
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
1828896 S.P.Eisenberg, M.T.Brewer, E.Verderber, P.Heimdal, B.J.Brandhuber, and R.C.Thompson (1991).
Interleukin 1 receptor antagonist is a member of the interleukin 1 gene family: evolution of a cytokine control mechanism.
  Proc Natl Acad Sci U S A, 88, 5232-5236.  
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.