PDBsum entry: 1i1b

Cytokine

PDB-id

1i1b

Contents

Description

Header details

Protein chain

Waters ×83

* Residue conservation analysis

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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

UniProt:

P01584 (IL1B_HUMAN)

Seq:

269 a.a.

Struc:

151 a.a.

Key:		PfamA domain
		Secondary structure			CATH domain

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

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Key reference

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

PubMed id Reference

18798567 L.Maveyraud, H.Niwa, V.Guillet, D.I.Svergun, P.V.Konarev, R.A.Palmer, W.J.Peumans, P.Rougé, E.J.Van Damme, C.D.Reynolds, and L.Mourey (2009).
Structural basis for sugar recognition, including the Tn carcinoma antigen, by the lectin SNA-II from Sambucus nigra.

Proteins, 75, 89.

PDB codes: 3c9z 3ca0 3ca1 3ca3 3ca4 3ca5 3ca6 3cah

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

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

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.

17590957 J.R.Hea, S.Bino, G.W.Roberts, J.G.Raynes, and A.D.Miller (2002).
Mechanistic investigation into complementary (antisense) peptide mini-receptor inhibitors of cytokine interleukin-1.

Chembiochem, 3, 76-85.

11093146 J.L.Barton, R.Herbst, D.Bosisio, L.Higgins, and M.J.Nicklin (2000).
A tissue specific IL-1 receptor antagonist homolog from the IL-1 cluster lacks IL-1, IL-1ra, IL-18 and IL-18 antagonist activities.

Eur J Immunol, 30, 3299-3308.

10748229 Y.Liu, A.J.Chirino, Z.Misulovin, C.Leteux, T.Feizi, M.C.Nussenzweig, and P.J.Bjorkman (2000).
Crystal structure of the cysteine-rich domain of mannose receptor complexed with a sulfated carbohydrate ligand.

J Exp Med, 191, 1105-1116.

PDB codes: 1dqg 1dqo

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

10082365 T.D.Osslund, R.Syed, E.Singer, E.W.Hsu, R.Nybo, B.L.Chen, T.Harvey, T.Arakawa, L.O.Narhi, A.Chirino, and C.F.Morris (1998).
Correlation between the 1.6 A crystal structure and mutational analysis of keratinocyte growth factor.

Protein Sci, 7, 1681-1690.

9241431 C.Chothia, T.Hubbard, S.Brenner, H.Barns, and A.Murzin (1997).
Protein folds in the all-beta and all-alpha classes.

Annu Rev Biophys Biomol Struct, 26, 597-627.

9334739 T.R.Transue, A.K.Smith, H.Mo, I.J.Goldstein, and M.A.Saper (1997).
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).
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.

9162944 L.Zhang, and J.Hermans (1996).
Hydrophilicity of cavities in proteins.

Proteins, 24, 433-438.

8652550 M.Blaber, J.DiSalvo, and K.A.Thomas (1996).
X-ray crystal structure of human acidic fibroblast growth factor.

Biochemistry, 35, 2086-2094.

PDB code: 1afg

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.

J Comput Aided Mol Des, 10, 558-566.

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

7773181 M.B.Swindells (1995).
A procedure for the automatic determination of hydrophobic cores in protein structures.

Protein Sci, 4, 93.

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).
Insertion of a structural domain of interleukin (IL)-1 beta confers agonist activity to the IL-1 receptor antagonist. Implications for IL-1 bioactivity.

J Biol Chem, 270, 22460-22466.

7499244 U.Kavita, and S.B.Mizel (1995).
Differential sensitivity of interleukin-1 alpha and -beta precursor proteins to cleavage by calpain, a calcium-dependent protease.

J Biol Chem, 270, 27758-27765.

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.

Protein Sci, 3, 372-390.

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 code: 1fga

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.

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.

J Protein Chem, 11, 709-722.

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.

1388674 P.Manavalan, D.L.Swope, and R.M.Withy (1992).
Sequence and structural relationships in the cytokine family.

J Protein Chem, 11, 321-331.

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.

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.