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Cytokine PDB id
7i1b
Jmol
Contents
Protein chain
153 a.a. *
Waters ×21
* Residue conservation analysis
PDB id:
7i1b
Name: Cytokine
Title: High-resolution three-dimensional structure of interleukin- 1 beta in solution by three-and four-dimensional nuclear magnetic resonance spectroscopy
Structure: Interleukin-1 beta. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
NMR struc: 32 models
Authors: G.M.Clore,A.M.Gronenborn
Key ref:
G.M.Clore et al. (1991). High-resolution three-dimensional structure of interleukin 1 beta in solution by three- and four-dimensional nuclear magnetic resonance spectroscopy. Biochemistry, 30, 2315-2323. PubMed id: 2001363 DOI: 10.1021/bi00223a005
Date:
22-Jan-91     Release date:   15-Oct-92    
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     growth factor activity     2 terms  

 

 
DOI no: 10.1021/bi00223a005 Biochemistry 30:2315-2323 (1991)
PubMed id: 2001363  
 
 
High-resolution three-dimensional structure of interleukin 1 beta in solution by three- and four-dimensional nuclear magnetic resonance spectroscopy.
G.M.Clore, P.T.Wingfield, A.M.Gronenborn.
 
  ABSTRACT  
 
The determination of the high-resolution three-dimensional solution structure of interleukin 1 beta (IL-1 beta), a protein of 153 residues and 17.4 kDa, which plays a central role in the immune and inflammatory responses, has been determined by heteronuclear (13C and 15N) three- and four-dimensional NMR spectroscopy. The structure is based on 3146 experimental restraints comprising 2780 distance and 366 torsion angle (phi, psi, and chi 1) restraints. A total of 32 simulated annealing structures are calculated, and the atomic RMS distribution about the mean coordinate positions is 0.41 +/- 0.04 A for the backbone atoms and 0.82 +/- 0.04 A for all atoms (excluding residue 1 at the N-terminus and residues 152 and 153 at the C-terminus, which are partially disordered). In the case of internal side chains with a surface accessibility of less than or equal to 40%, the atomic RMS distribution about the mean coordinate positions for all atoms is 0.49 +/- 0.03 A. IL-1 beta resembles a tetrahedron and is composed of 12 beta-strands arranged in three pseudosymmetric topological units, each of which comprises 5 strands. Analysis of the mutational data on IL-1 beta in the light of the three-dimensional structure suggests the presence of three distinct binding sites for the IL-1 receptor on the surface of the protein. It is suggested that each of the three immunoglobulin domains which comprise the extracellular portion of the IL-1 receptor recognizes one of these sites.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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Pro-interleukin (IL)-1beta shares a core region of stability as compared with mature IL-1beta while maintaining a distinctly different configurational landscape: a comparative hydrogen/deuterium exchange mass spectrometry study.
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PDB code: 2nvh
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PDB codes: 1u2f 2u2f
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The structure of versutoxin (delta-atracotoxin-Hv1) provides insights into the binding of site 3 neurotoxins to the voltage-gated sodium channel.
  Structure, 5, 1525-1535.
PDB code: 1vtx
9228949 J.I.Fletcher, R.Smith, S.I.O'Donoghue, M.Nilges, M.Connor, M.E.Howden, M.J.Christie, and G.F.King (1997).
The structure of a novel insecticidal neurotoxin, omega-atracotoxin-HV1, from the venom of an Australian funnel web spider.
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PDB code: 1axh
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.
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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.
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8575189 A.M.Gronenborn, and G.M.Clore (1995).
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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
  8528076 R.S.DeWitte, S.W.Michnick, and E.I.Shakhnovich (1995).
Exhaustive enumeration of protein conformations using experimental restraints.
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7673234 S.A.Greenfeder, T.Varnell, G.Powers, K.Lombard-Gillooly, D.Shuster, K.W.McIntyre, D.E.Ryan, W.Levin, V.Madison, and G.Ju (1995).
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7608192 W.M.Siders, and S.B.Mizel (1995).
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High-resolution structure of Ascaris trypsin inhibitor in solution: direct evidence for a pH-induced conformational transition in the reactive site.
  Structure, 2, 669-678.
PDB codes: 1ata 1atb 1atd 1ate
  8019409 G.M.Clore, and A.M.Gronenborn (1994).
Young Investigator Award Lecture. Structures of larger proteins, protein-ligand and protein-DNA complexes by multidimensional heteronuclear NMR.
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Mutations and off-pathway aggregation of proteins.
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8183906 S.Bagby, T.S.Harvey, S.G.Eagle, S.Inouye, and M.Ikura (1994).
Structural similarity of a developmentally regulated bacterial spore coat protein to beta gamma-crystallins of the vertebrate eye lens.
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8210313 A.T.Brünger, and M.Nilges (1993).
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8513791 F.K.Junius, A.S.Weiss, and G.F.King (1993).
The solution structure of the leucine zipper motif of the Jun oncoprotein homodimer.
  Eur J Biochem, 214, 415-424.  
  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.
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8272428 P.Herzyk, and R.E.Hubbard (1993).
A reduced representation of proteins for use in restraint satisfaction calculations.
  Proteins, 17, 310-324.  
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
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.  
  1369391 P.R.Young (1992).
Protein hormones and their receptors.
  Curr Opin Biotechnol, 3, 408-421.  
1392567 S.Ludvigsen, and F.M.Poulsen (1992).
Positive theta-angles in proteins by nuclear magnetic resonance spectroscopy.
  J Biomol NMR, 2, 227-233.  
  1368432 W.J.Chazin (1992).
NMR structures and methodology.
  Curr Opin Biotechnol, 3, 326-332.  
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.  
1668718 G.M.Clore, A.Bax, and A.M.Gronenborn (1991).
Stereospecific assignment of beta-methylene protons in larger proteins using 3D 15N-separated Hartmann-Hahn and 13C-separated rotating frame Overhauser spectroscopy.
  J Biomol NMR, 1, 13-22.  
1668724 Y.Gao, N.C.Veitch, and R.J.Williams (1991).
The value of chemical shift parameters in the description of protein solution structures.
  J Biomol NMR, 1, 457-471.  
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.