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PDBsum entry 3il8

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protein links
Cytokine PDB id
3il8
Jmol PyMol
Contents
Protein chain
68 a.a. *
Waters ×135
* Residue conservation analysis
PDB id:
3il8
Name: Cytokine
Title: Crystal structure of interleukin 8: symbiosis of nmr and crystallography
Structure: Interleukin-8. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Organ: neutrophils
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.187    
Authors: E.T.Baldwin,I.T.Weber,R.St Charles,J.-C.Xuan,E.Appella,M.Yam K.Matsushima,B.F.P.Edwards,G.M.Clore,A.M.Gronenborn,A.Wloda
Key ref: E.T.Baldwin et al. (1991). Crystal structure of interleukin 8: symbiosis of NMR and crystallography. Proc Natl Acad Sci U S A, 88, 502-506. PubMed id: 1988949 DOI: 10.1073/pnas.88.2.502
Date:
07-Dec-90     Release date:   15-Oct-92    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P10145  (IL8_HUMAN) -  Interleukin-8
Seq:
Struc:
99 a.a.
68 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   3 terms 
  Biological process     intracellular signal transduction   31 terms 
  Biochemical function     protein binding     4 terms  

 

 
DOI no: 10.1073/pnas.88.2.502 Proc Natl Acad Sci U S A 88:502-506 (1991)
PubMed id: 1988949  
 
 
Crystal structure of interleukin 8: symbiosis of NMR and crystallography.
E.T.Baldwin, I.T.Weber, R.St Charles, J.C.Xuan, E.Appella, M.Yamada, K.Matsushima, B.F.Edwards, G.M.Clore, A.M.Gronenborn.
 
  ABSTRACT  
 
The crystal structure of a host defense system chemotactic factor, interleukin 8, has been solved by molecular replacement using as a model the solution structure derived from nuclear magnetic resonance experiments. The structure was refined with 2 A x-ray data to an R factor of 0.187 (0.217 at 1.6 A). A comparison indicates some potential differences between the structure in solution and in the crystalline state. Our analysis also predicts that residues 4 through 9 on the amino terminus and the beta-bend, which includes His-33, may be important for receptor binding.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21377040 M.Akdis, S.Burgler, R.Crameri, T.Eiwegger, H.Fujita, E.Gomez, S.Klunker, N.Meyer, L.O'Mahony, O.Palomares, C.Rhyner, N.Quaked, A.Schaffartzik, W.Van De Veen, S.Zeller, M.Zimmermann, and C.A.Akdis (2011).
Interleukins, from 1 to 37, and interferon-γ: receptors, functions, and roles in diseases.
  J Allergy Clin Immunol, 127, 701.  
18971938 C.J.Liu, Y.J.Huang, H.L.Chen, H.T.Lin, H.L.Lin, M.L.Kuo, J.L.Huang, D.S.Chen, P.J.Chen, and H.L.Wu (2009).
Characterization of interleukin 8 in woodchucks with chronic hepatitis B and hepatocellular carcinoma.
  Genes Immun, 10, 27-36.  
19578117 J.Hol, A.M.Küchler, F.E.Johansen, B.Dalhus, G.Haraldsen, and I.Oynebråten (2009).
Molecular requirements for sorting of the chemokine interleukin-8/CXCL8 to endothelial Weibel-Palade bodies.
  J Biol Chem, 284, 23532-23539.  
19477417 M.Kapoor, F.J.Otero, B.M.Slike, K.L.Ewalt, and X.L.Yang (2009).
Mutational separation of aminoacylation and cytokine activities of human tyrosyl-tRNA synthetase.
  Chem Biol, 16, 531-539.  
19813761 S.Bourbigot, L.Fardy, A.J.Waring, M.R.Yeaman, and V.Booth (2009).
Structure of chemokine-derived antimicrobial Peptide interleukin-8alpha and interaction with detergent micelles and oriented lipid bilayers.
  Biochemistry, 48, 10509-10521.  
18816799 T.A.Ramelot, S.Raman, A.P.Kuzin, R.Xiao, L.C.Ma, T.B.Acton, J.F.Hunt, G.T.Montelione, D.Baker, and M.A.Kennedy (2009).
Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study.
  Proteins, 75, 147-167.
PDB codes: 1tvg 1xpw
18786394 M.Nilges, A.Bernard, B.Bardiaux, T.Malliavin, M.Habeck, and W.Rieping (2008).
Accurate NMR structures through minimization of an extended hybrid energy.
  Structure, 16, 1305-1312.  
17876799 N.Huynh, B.Mallik, L.Zhang, M.Martins-Green, and D.Morikis (2008).
Computational studies of CXCR1, the receptor of IL-8/CXCL8, using molecular dynamics and electrostatics.
  Biopolymers, 89, 52-61.  
18560148 T.Jabeen, P.Leonard, H.Jamaluddin, and K.R.Acharya (2008).
Structure of mouse IP-10, a chemokine.
  Acta Crystallogr D Biol Crystallogr, 64, 611-619.
PDB code: 2r3z
17222184 H.Fernando, G.T.Nagle, and K.Rajarathnam (2007).
Thermodynamic characterization of interleukin-8 monomer binding to CXCR1 receptor N-terminal domain.
  FEBS J, 274, 241-251.  
17334823 K.H.Kim (2007).
Outliers in SAR and QSAR: is unusual binding mode a possible source of outliers?
  J Comput Aided Mol Des, 21, 63-86.  
17024463 R.David, and A.G.Beck-Sickinger (2007).
Identification of the dimerisation interface of human interleukin-8 by IL-8-variants containing the photoactivatable amino acid benzoyl-phenylalanine.
  Eur Biophys J, 36, 385-391.  
17243149 Y.Li, D.Liu, R.Cao, S.Kumar, C.Dong, J.An, S.R.Wilson, Y.G.Gao, and Z.Huang (2007).
Crystal structure of chemically synthesized vMIP-II.
  Proteins, 67, 243-246.
PDB codes: 2fht 2fj2
16806458 C.A.Howell, S.R.Sandeman, G.J.Phillips, A.W.Lloyd, J.G.Davies, S.V.Mikhalovsky, S.R.Tennison, A.P.Rawlinson, O.P.Kozynchenko, H.L.Owen, J.D.Gaylor, J.J.Rouse, and J.M.Courtney (2006).
The in vitro adsorption of cytokines by polymer-pyrolysed carbon.
  Biomaterials, 27, 5286-5291.  
16678487 C.Weber, and R.R.Koenen (2006).
Fine-tuning leukocyte responses: towards a chemokine 'interactome'.
  Trends Immunol, 27, 268-273.  
16474398 N.M.Weathington, A.H.van Houwelingen, B.D.Noerager, P.L.Jackson, A.D.Kraneveld, F.S.Galin, G.Folkerts, F.P.Nijkamp, and J.E.Blalock (2006).
A novel peptide CXCR ligand derived from extracellular matrix degradation during airway inflammation.
  Nat Med, 12, 317-323.  
16736494 N.Y.Yount, A.S.Bayer, Y.Q.Xiong, and M.R.Yeaman (2006).
Advances in antimicrobial peptide immunobiology.
  Biopolymers, 84, 435-458.  
  16820679 Z.A.Malik, and B.F.Tack (2006).
Structure of human MIP-3alpha chemokine.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 631-634.
PDB code: 2hci
16127067 A.Björstad, H.Fu, A.Karlsson, C.Dahlgren, and J.Bylund (2005).
Interleukin-8-derived peptide has antibacterial activity.
  Antimicrob Agents Chemother, 49, 3889-3895.  
15852307 C.S.Rapp, and R.M.Pollack (2005).
Crystal packing effects on protein loops.
  Proteins, 60, 103-109.  
15618397 J.Klein, and N.Nikolaidis (2005).
The descent of the antibody-based immune system by gradual evolution.
  Proc Natl Acad Sci U S A, 102, 169-174.  
15979374 J.Y.Springael, E.Urizar, and M.Parmentier (2005).
Dimerization of chemokine receptors and its functional consequences.
  Cytokine Growth Factor Rev, 16, 611-623.  
15803062 M.A.Williams, C.M.Cave, G.Quaid, C.Robinson, T.J.Daly, D.Witt, A.B.Lentsch, and J.S.Solomkin (2005).
Interleukin 8 dimerization as a mechanism for regulation of neutrophil adherence-dependent oxidant production.
  Shock, 23, 371-376.  
14997572 E.Krieger, E.Geretti, B.Brandner, B.Goger, T.N.Wells, and A.J.Kungl (2004).
A structural and dynamic model for the interaction of interleukin-8 and glycosaminoglycans: support from isothermal fluorescence titrations.
  Proteins, 54, 768-775.  
12737818 G.J.Swaminathan, D.E.Holloway, R.A.Colvin, G.K.Campanella, A.C.Papageorgiou, A.D.Luster, and K.R.Acharya (2003).
Crystal structures of oligomeric forms of the IP-10/CXCL10 chemokine.
  Structure, 11, 521-532.
PDB codes: 1o7y 1o7z 1o80
14719805 R.David, Z.Machova, and A.G.Beck-Sickinger (2003).
Semisynthesis and application of carboxyfluorescein-labelled biologically active human interleukin-8.
  Biol Chem, 384, 1619-1630.  
14709826 T.Itou, Y.Yoshida, Y.Shoji, H.Sugisawa, T.Endo, and T.Sakai (2003).
Molecular cloning and expression of bottlenose dolphin (Tursiops truncatus) interleukin-8.
  J Vet Med Sci, 65, 1351-1354.  
12081625 D.J.Gordon, R.Tappe, and S.C.Meredith (2002).
Design and characterization of a membrane permeable N-methyl amino acid-containing peptide that inhibits Abeta1-40 fibrillogenesis.
  J Pept Res, 60, 37-55.  
11807180 E.J.Fernandez, and E.Lolis (2002).
Structure, function, and inhibition of chemokines.
  Annu Rev Pharmacol Toxicol, 42, 469-499.  
  11999552 S.Starckx, P.E.Van den Steen, A.Wuyts, J.Van Damme, and G.Opdenakker (2002).
Neutrophil gelatinase B and chemokines in leukocytosis and stem cell mobilization.
  Leuk Lymphoma, 43, 233-241.  
11276368 M.Crow, D.D.Taub, S.Cooper, H.E.Broxmeyer, and A.H.Sarris (2001).
Human recombinant interferon-inducible protein-10: intact disulfide bridges are not required for inhibition of hematopoietic progenitors and chemotaxis of T lymphocytes and monocytes.
  J Hematother Stem Cell Res, 10, 147-156.  
11567160 Y.W.Chen (2001).
Solution solution: using NMR models for molecular replacement.
  Acta Crystallogr D Biol Crystallogr, 57, 1457-1461.  
  11152129 Buyong, J.Xiong, J.Lubkowski, and R.Nussinov (2000).
Homology modeling and molecular dynamics simulations of lymphotactin.
  Protein Sci, 9, 2192-2199.  
11087354 J.Blaszczyk, E.V.Coillie, P.Proost, J.V.Damme, G.Opdenakker, G.D.Bujacz, J.M.Wang, and X.Ji (2000).
Complete crystal structure of monocyte chemotactic protein-2, a CC chemokine that interacts with multiple receptors.
  Biochemistry, 39, 14075-14081.
PDB code: 1esr
10727234 J.S.Laurence, C.Blanpain, J.W.Burgner, M.Parmentier, and P.J.LiWang (2000).
CC chemokine MIP-1 beta can function as a monomer and depends on Phe13 for receptor binding.
  Biochemistry, 39, 3401-3409.  
10707023 N.Gerber, H.Lowman, D.R.Artis, and C.Eigenbrot (2000).
Receptor-binding conformation of the "ELR" motif of IL-8: X-ray structure of the L5C/H33C variant at 2.35 A resolution.
  Proteins, 38, 361-367.
PDB code: 1qe6
10954912 Y.Ohnishi, T.Senda, N.Nandhagopal, K.Sugimoto, T.Shioda, Y.Nagal, and Y.Mitsui (2000).
Crystal structure of recombinant native SDF-1alpha with additional mutagenesis studies: an attempt at a more comprehensive interpretation of accumulated structure-activity relationship data.
  J Interferon Cytokine Res, 20, 691-700.
PDB code: 1qg7
11080645 Y.W.Chen, E.J.Dodson, and G.J.Kleywegt (2000).
Does NMR mean "not for molecular replacement"? Using NMR-based search models to solve protein crystal structures.
  Structure, 8, R213-R220.  
11092918 Y.W.Chen, and G.M.Clore (2000).
A systematic case study on using NMR models for molecular replacement: p53 tetramerization domain revisited.
  Acta Crystallogr D Biol Crystallogr, 56, 1535-1540.  
10320325 H.Sticht, S.E.Escher, K.Schweimer, W.G.Forssmann, P.Rösch, and K.Adermann (1999).
Solution structure of the human CC chemokine 2: A monomeric representative of the CC chemokine subtype.
  Biochemistry, 38, 5995-6002.
PDB code: 2hcc
10398929 K.P.Murphy (1999).
Predicting binding energetics from structure: looking beyond DeltaG degrees.
  Med Res Rev, 19, 333-339.  
  10196260 M.R.MacDonald, M.W.Burney, S.B.Resnick, and I.V.Virgin HW (1999).
Spliced mRNA encoding the murine cytomegalovirus chemokine homolog predicts a beta chemokine of novel structure.
  J Virol, 73, 3682-3691.  
10089391 S.Gourinath, A.Srinivasan, and T.P.Singh (1999).
Structure of the bifunctional inhibitor of trypsin and alpha-amylase from ragi seeds at 2.9 A resolution.
  Acta Crystallogr D Biol Crystallogr, 55, 25-30.
PDB code: 1jfo
9485384 J.Inglese, P.Samama, S.Patel, J.Burbaum, I.L.Stroke, and K.C.Appell (1998).
Chemokine receptor-ligand interactions measured using time-resolved fluorescence.
  Biochemistry, 37, 2372-2377.  
9461080 J.Lubkowski, F.Hennecke, A.Plückthun, and A.Wlodawer (1998).
The structural basis of phage display elucidated by the crystal structure of the N-terminal domains of g3p.
  Nat Struct Biol, 5, 140-147.
PDB code: 1g3p
9788958 M.C.Gershengorn, E.Geras-Raaka, A.Varma, and I.Clark-Lewis (1998).
Chemokines activate Kaposi's sarcoma-associated herpesvirus G protein-coupled receptor in mammalian cells in culture.
  J Clin Invest, 102, 1469-1472.  
9309221 C.T.Farrar, C.J.Halkides, and D.J.Singel (1997).
The frozen solution structure of p21 ras determined by ESEEM spectroscopy reveals weak coordination of Thr35 to the active site metal ion.
  Structure, 5, 1055-1066.  
9136886 E.Ilyina, V.Roongta, and K.H.Mayo (1997).
NMR structure of a de novo designed, peptide 33mer with two distinct, compact beta-sheet folds.
  Biochemistry, 36, 5245-5250.  
9393669 G.McFadden, and D.Kelvin (1997).
New strategies for chemokine inhibition and modulation: you take the high road and I'll take the low road.
  Biochem Pharmacol, 54, 1271-1280.  
  9070442 H.B.Lowman, W.J.Fairbrother, P.H.Slagle, R.Kabakoff, J.Liu, S.Shire, and C.A.Hébert (1997).
Monomeric variants of IL-8: effects of side chain substitutions and solution conditions upon dimer formation.
  Protein Sci, 6, 598-608.  
8989326 J.Lubkowski, G.Bujacz, L.Boqué, P.J.Domaille, T.M.Handel, and A.Wlodawer (1997).
The structure of MCP-1 in two crystal forms provides a rare example of variable quaternary interactions.
  Nat Struct Biol, 4, 64-69.
PDB codes: 1dok 1dol
9143704 M.Baggiolini, B.Dewald, and B.Moser (1997).
Human chemokines: an update.
  Annu Rev Immunol, 15, 675-705.  
9109648 S.Meunier, J.M.Bernassau, J.C.Guillemot, P.Ferrara, and H.Darbon (1997).
Determination of the three-dimensional structure of CC chemokine monocyte chemoattractant protein 3 by 1H two-dimensional NMR spectroscopy.
  Biochemistry, 36, 4412-4422.
PDB code: 1ncv
  9070443 S.R.Leong, H.B.Lowman, J.Liu, S.Shire, L.E.Deforge, B.L.Gillece-Castro, R.McDowell, and C.A.Hébert (1997).
IL-8 single-chain homodimers and heterodimers: interactions with chemokine receptors CXCR1, CXCR2, and DARC.
  Protein Sci, 6, 609-617.  
8631339 H.Sticht, M.Auer, B.Schmitt, J.Besemer, M.Horcher, T.Kirsch, I.J.Lindley, and P.Rösch (1996).
Structure and activity of a chimeric interleukin-8-melanoma-growth-stimulatory-activity protein.
  Eur J Biochem, 235, 26-35.
PDB code: 1rod
8643551 H.W.Sun, J.Bernhagen, R.Bucala, and E.Lolis (1996).
Crystal structure at 2.6-A resolution of human macrophage migration inhibitory factor.
  Proc Natl Acad Sci U S A, 93, 5191-5196.
PDB code: 1mif
8913681 J.P.Turkenburg, and E.J.Dodson (1996).
Modern developments in molecular replacement.
  Curr Opin Struct Biol, 6, 604-610.  
  8819163 K.H.Mayo, E.Ilyina, and H.Park (1996).
A recipe for designing water-soluble, beta-sheet-forming peptides.
  Protein Sci, 5, 1301-1315.  
8605628 M.Suzuki, H.Sugimoto, A.Nakagawa, I.Tanaka, J.Nishihira, and M.Sakai (1996).
Crystal structure of the macrophage migration inhibitory factor from rat liver.
  Nat Struct Biol, 3, 259-266.
PDB code: 1fim
  7796798 N.Q.McDonald, N.Panayotatos, and W.A.Hendrickson (1995).
Crystal structure of dimeric human ciliary neurotrophic factor determined by MAD phasing.
  EMBO J, 14, 2689-2699.
PDB code: 1cnt
  7651403 Y.Zhang, and B.J.Rollins (1995).
A dominant negative inhibitor indicates that monocyte chemoattractant protein 1 functions as a dimer.
  Mol Cell Biol, 15, 4851-4855.  
8069631 D.A.Rozwarski, A.M.Gronenborn, G.M.Clore, J.F.Bazan, A.Bohm, A.Wlodawer, M.Hatada, and P.A.Karplus (1994).
Structural comparisons among the short-chain helical cytokines.
  Structure, 2, 159-173.  
  7703852 D.G.Covell, G.W.Smythers, A.M.Gronenborn, and G.M.Clore (1994).
Analysis of hydrophobicity in the alpha and beta chemokine families and its relevance to dimerization.
  Protein Sci, 3, 2064-2072.  
  8164648 J.N.Heinrich, E.C.O'Rourke, L.Chen, H.Gray, K.S.Dorfman, and R.Bravo (1994).
Biological activity of the growth factor-induced cytokine N51: structure-function analysis using N51/Interleukin-8 chimeric molecules.
  Mol Cell Biol, 14, 2849-2861.  
8210313 A.T.Brünger, and M.Nilges (1993).
Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR-spectroscopy.
  Q Rev Biophys, 26, 49.  
  8401223 A.Wlodawer, A.Pavlovsky, and A.Gustchina (1993).
Hematopoietic cytokines: similarities and differences in the structures, with implications for receptor binding.
  Protein Sci, 2, 1373-1382.  
  8221207 C.A.Hébert, and J.B.Baker (1993).
Interleukin-8: a review.
  Cancer Invest, 11, 743-750.  
8335079 H.Bang, K.Brune, C.Nager, and U.Feige (1993).
Interleukin-8 is a cyclosporin A binding protein.
  Experientia, 49, 533-538.  
8475106 I.Clark-Lewis, B.Dewald, T.Geiser, B.Moser, and M.Baggiolini (1993).
Platelet factor 4 binds to interleukin 8 receptors and activates neutrophils when its N terminus is modified with Glu-Leu-Arg.
  Proc Natl Acad Sci U S A, 90, 3574-3577.  
8346230 L.M.Webb, M.U.Ehrengruber, I.Clark-Lewis, M.Baggiolini, and A.Rot (1993).
Binding to heparan sulfate or heparin enhances neutrophil responses to interleukin 8.
  Proc Natl Acad Sci U S A, 90, 7158-7162.  
8272427 M.Nilges (1993).
A calculation strategy for the structure determination of symmetric dimers by 1H NMR.
  Proteins, 17, 297-309.  
8234243 W.J.Chuang, D.J.Weber, A.G.Gittis, and A.S.Mildvan (1993).
Mutational tests of the NMR-docked structure of the staphylococcal nuclease-metal-3',5'-pdTp complex.
  Proteins, 17, 36-48.  
1511746 A.Wlodawer, A.Wlodaver, A.Pavlovsky, and A.Gustchina (1992).
Crystal structure of human recombinant interleukin-4 at 2.25 A resolution.
  FEBS Lett, 309, 59-64.
PDB code: 1rcb
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.  
1409574 J.A.Stuckey, R.St Charles, and B.F.Edwards (1992).
A model of the platelet factor 4 complex with heparin.
  Proteins, 14, 277-287.  
1639201 M.Baggiolini, and I.Clark-Lewis (1992).
Interleukin-8, a chemotactic and inflammatory cytokine.
  FEBS Lett, 307, 97.  
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.  
1557400 M.D.Miller, and M.S.Krangel (1992).
The human cytokine I-309 is a monocyte chemoattractant.
  Proc Natl Acad Sci U S A, 89, 2950-2954.  
1528078 M.D.Walkinshaw (1992).
Protein targets for structure-based drug design.
  Med Res Rev, 12, 317-372.  
  1325984 M.Martins-Green, A.Aotaki-Keen, L.M.Hjelmeland, and M.J.Bissell (1992).
The 9E3 protein: immunolocalization in vivo and evidence for multiple forms in culture.
  J Cell Sci, 101, 701-707.  
  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
1438200 W.Braun, M.Vasák, A.H.Robbins, C.D.Stout, G.Wagner, J.H.Kägi, and K.Wüthrich (1992).
Comparison of the NMR solution structure and the x-ray crystal structure of rat metallothionein-2.
  Proc Natl Acad Sci U S A, 89, 10124-10128.
PDB code: 4mt2
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.

 

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