PDBsum entry 1tnf

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protein Protein-protein interface(s) links
Lymphokine PDB id
Protein chains
152 a.a. *
* Residue conservation analysis
PDB id:
Name: Lymphokine
Title: The structure of tumor necrosis factor-alpha at 2.6 angstroms resolution. Implications for receptor binding
Structure: Tumor necrosis factor-alpha. Chain: a, b, c. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
Biol. unit: Trimer (from PQS)
2.60Å     R-factor:   0.230    
Authors: M.J.Eck,S.R.Sprang
Key ref: M.J.Eck and S.R.Sprang (1989). The structure of tumor necrosis factor-alpha at 2.6 A resolution. Implications for receptor binding. J Biol Chem, 264, 17595-17605. PubMed id: 2551905
25-Aug-89     Release date:   15-Jan-90    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P01375  (TNFA_HUMAN) -  Tumor necrosis factor
233 a.a.
152 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biological process     immune response   1 term 
  Biochemical function     tumor necrosis factor receptor binding     1 term  


J Biol Chem 264:17595-17605 (1989)
PubMed id: 2551905  
The structure of tumor necrosis factor-alpha at 2.6 A resolution. Implications for receptor binding.
M.J.Eck, S.R.Sprang.
The three-dimensional structure of tumor necrosis factor (TNF-alpha), a protein hormone secreted by macrophages, has been determined at 2.6 A resolution by x-ray crystallography. Phases were determined by multiple isomorphous replacement using data collected from five heavy atom derivatives. The multiple isomorphous replacement phases were further improved by real space symmetry averaging, exploiting the noncrystallographic 3-fold symmetry of the TNF-alpha trimer. An atomic model corresponding to the known amino acid sequence of TNF-alpha was readily built into the electron density map calculated with these improved phases. The 17,350-dalton monomer forms an elongated, antiparallel beta-pleated sheet sandwich with a "jelly-roll" topology. Three monomers associate intimately about a 3-fold axis of symmetry to form a compact bell-shaped trimer. Examination of the model and comparison to known protein structures reveals striking structural homology to several viral coat proteins, particularly satellite tobacco necrosis virus. Locations of residues conserved between TNF-alpha and lymphotoxin (TNF-beta, a related cytokine known to bind to the same receptors as TNF-alpha) suggest that lymphotoxin, like TNF-alpha, binds to the receptor as a trimer and that the general site of interaction with the receptor is at the "base" of the trimer.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20571888 P.Kleinbongard, R.Schulz, and G.Heusch (2011).
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21088666 S.G.Hymowitz, and V.M.Dixit (2010).
Unleashing cell death: the Fas-FADD complex.
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20303167 S.Yachamaneni, G.Yushin, S.H.Yeon, Y.Gogotsi, C.Howell, S.Sandeman, G.Phillips, and S.Mikhalovsky (2010).
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Biochemical and structural characterization of the human TL1A ectodomain.
  Biochemistry, 48, 7636-7645.
PDB codes: 2qe3 2rjk 2rjl
19426226 G.Cai, and G.J.Freeman (2009).
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19027157 S.Haider, and M.Knöfler (2009).
Human tumour necrosis factor: physiological and pathological roles in placenta and endometrium.
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Fast binding kinetics and conserved 3D structure underlie the antagonistic activity of mutant TNF: useful information for designing artificial proteo-antagonists.
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PDB code: 2zpx
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Evolution of GITRL immune function: murine GITRL exhibits unique structural and biochemical properties within the TNF superfamily.
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PDB codes: 2qdn 3b9i
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Assembly and structural properties of glucocorticoid-induced TNF receptor ligand: Implications for function.
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PDB codes: 2q1m 2r30 2r32
17502864 R.S.Wallis (2007).
Reactivation of latent tuberculosis by TNF blockade: the role of interferon gamma.
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A TNF receptor loop peptide mimic blocks RANK ligand-induced signaling, bone resorption, and bone loss.
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16423863 T.L.O'Loughlin, D.N.Greene, and I.Matsumura (2006).
Diversification and specialization of HIV protease function during in vitro evolution.
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16340415 M.B.Yaffe (2005).
X-ray crystallography and structural biology.
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Ligands working as receptors: reverse signaling by members of the TNF superfamily enhance the plasticity of the immune system.
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Tumor necrosis factor family ligand-receptor binding.
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15562003 T.Mori, A.Oguro, T.Ohtsu, and Y.Nakamura (2004).
RNA aptamers selected against the receptor activator of NF-kappaB acquire general affinity to proteins of the tumor necrosis factor receptor family.
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15364058 U.Kishore, C.Gaboriaud, P.Waters, A.K.Shrive, T.J.Greenhough, K.B.Reid, R.B.Sim, and G.J.Arlaud (2004).
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Recombinant single-chain antibody fusion construct targeting human melanoma cells and containing tumor necrosis factor.
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[Creation of functional muteins using phage libraries for pharmacoproteomic-based drug discovery and development of DDS]
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Biological functions of tumor necrosis factor cytokines and their receptors.
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12721620 Y.Liu, X.Hong, J.Kappler, L.Jiang, R.Zhang, L.Xu, C.H.Pan, W.E.Martin, R.C.Murphy, H.B.Shu, S.Dai, and G.Zhang (2003).
Ligand-receptor binding revealed by the TNF family member TALL-1.
  Nature, 423, 49-56.
PDB codes: 1oqd 1oqe
12189384 A.Ashkenazi (2002).
Targeting death and decoy receptors of the tumour-necrosis factor superfamily.
  Nat Rev Cancer, 2, 420-430.  
11862220 D.A.Oren, Y.Li, Y.Volovik, T.S.Morris, C.Dharia, K.Das, O.Galperina, R.Gentz, and E.Arnold (2002).
Structural basis of BLyS receptor recognition.
  Nat Struct Biol, 9, 288-292.
PDB code: 1kxg
12392561 G.H.Nam, and K.Y.Choi (2002).
Association of human tumor necrosis factor-related apoptosis inducing ligand with membrane upon acidification.
  Eur J Biochem, 269, 5280-5287.  
11796220 J.L.Bodmer, P.Schneider, and J.Tschopp (2002).
The molecular architecture of the TNF superfamily.
  Trends Biochem Sci, 27, 19-26.  
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Conjugation of a self-antigen to papillomavirus-like particles allows for efficient induction of protective autoantibodies.
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11237281 C.J.Capini, M.W.Richardson, H.Hendel, A.Sverstiuk, J.Mirchandani, E.G.Régulier, K.Khalili, J.F.Zagury, and J.Rappaport (2001).
Autoantibodies to TNFalpha in HIV-1 infection: prospects for anti-cytokine vaccine therapy.
  Biomed Pharmacother, 55, 23-31.  
11239407 R.M.Locksley, N.Killeen, and M.J.Lenardo (2001).
The TNF and TNF receptor superfamilies: integrating mammalian biology.
  Cell, 104, 487-501.  
11416205 Y.Chen, S.S.Molloy, L.Thomas, J.Gambee, H.P.Bächinger, B.Ferguson, J.Zonana, G.Thomas, and N.P.Morris (2001).
Mutations within a furin consensus sequence block proteolytic release of ectodysplasin-A and cause X-linked hypohidrotic ectodermal dysplasia.
  Proc Natl Acad Sci U S A, 98, 7218-7223.  
  12845748 C.Zhou, G.Shen, H.Zhu, J.Yang, Y.Zhang, J.Feng, and B.Shen (2000).
Construction and analysis of three-dimensional graphic model of single-chain Fv derived from an anti-human placental acidic isoferritin monoclonal antibody by computer.
  J Tongji Med Univ, 20, 23-25.  
11114500 E.Y.Jones (2000).
The tumour necrosis factor receptor family: life or death choices.
  Curr Opin Struct Biol, 10, 644-648.  
10891884 H.T.Idriss, and J.H.Naismith (2000).
TNF alpha and the TNF receptor superfamily: structure-function relationship(s).
  Microsc Res Tech, 50, 184-195.  
10908665 H.Ye, and H.Wu (2000).
Thermodynamic characterization of the interaction between TRAF2 and tumor necrosis factor receptor peptides by isothermal titration calorimetry.
  Proc Natl Acad Sci U S A, 97, 8961-8966.  
10651627 S.G.Hymowitz, M.P.O'Connell, M.H.Ultsch, A.Hurst, K.Totpal, A.Ashkenazi, Vos, and R.F.Kelley (2000).
A unique zinc-binding site revealed by a high-resolution X-ray structure of homotrimeric Apo2L/TRAIL.
  Biochemistry, 39, 633-640.
PDB code: 1dg6
10700560 S.J.Newman, B.Bond, B.Crook, J.Darker, C.Edge, and P.R.Maycox (2000).
Neuron-specific localisation of the TR3 death receptor in Alzheimer's disease.
  Brain Res, 857, 131-140.  
11057900 S.W.Fesik (2000).
Insights into programmed cell death through structural biology.
  Cell, 103, 273-282.  
  10211836 D.R.Westhead, T.W.Slidel, T.P.Flores, and J.M.Thornton (1999).
Protein structural topology: Automated analysis and diagrammatic representation.
  Protein Sci, 8, 897-904.  
10449196 F.Mancini, C.M.Toro, M.Mabilia, M.Giannangeli, M.Pinza, and C.Milanese (1999).
Inhibition of tumor necrosis factor-alpha (TNF-alpha)/TNF-alpha receptor binding by structural analogues of suramin.
  Biochem Pharmacol, 58, 851-859.  
10089307 K.J.Baeyens, H.L.De Bondt, A.Raeymaekers, W.Fiers, and C.J.De Ranter (1999).
The structure of mouse tumour-necrosis factor at 1.4 A resolution: towards modulation of its selectivity and trimerization.
  Acta Crystallogr D Biol Crystallogr, 55, 772-778.
PDB code: 2tnf
  10223910 N.S.Postma, R.C.Hermsen, D.J.Crommelin, W.M.Eling, and J.Zuidema (1999).
Thiolated recombinant human tumor necrosis factor-alpha protects against Plasmodium berghei K173-induced experimental cerebral malaria in mice.
  Antimicrob Agents Chemother, 43, 1027-1033.  
10382740 P.Schneider, R.Schwenzer, E.Haas, F.Mühlenbeck, G.Schubert, P.Scheurich, J.Tschopp, and H.Wajant (1999).
TWEAK can induce cell death via endogenous TNF and TNF receptor 1.
  Eur J Immunol, 29, 1785-1792.  
10549288 S.G.Hymowitz, H.W.Christinger, G.Fuh, M.Ultsch, M.O'Connell, R.F.Kelley, A.Ashkenazi, and Vos (1999).
Triggering cell death: the crystal structure of Apo2L/TRAIL in a complex with death receptor 5.
  Mol Cell, 4, 563-571.
PDB code: 1d0g
10216319 S.S.Cha, H.C.Shin, K.Y.Choi, and B.H.Oh (1999).
Expression, purification and crystallization of recombinant human TRAIL.
  Acta Crystallogr D Biol Crystallogr, 55, 1101-1104.  
10485660 S.S.Cha, M.S.Kim, Y.H.Choi, B.J.Sung, N.K.Shin, H.C.Shin, Y.C.Sung, and B.H.Oh (1999).
2.8 A resolution crystal structure of human TRAIL, a cytokine with selective antitumor activity.
  Immunity, 11, 253-261.
PDB code: 1d2q
10433725 S.S.Pullen, M.E.Labadia, R.H.Ingraham, S.M.McWhirter, D.S.Everdeen, T.Alber, J.J.Crute, and M.R.Kehry (1999).
High-affinity interactions of tumor necrosis factor receptor-associated factors (TRAFs) and CD40 require TRAF trimerization and CD40 multimerization.
  Biochemistry, 38, 10168-10177.  
9462508 D.N.Mauri, R.Ebner, R.I.Montgomery, K.D.Kochel, T.C.Cheung, G.L.Yu, S.Ruben, M.Murphy, R.J.Eisenberg, G.H.Cohen, P.G.Spear, and C.F.Ware (1998).
LIGHT, a new member of the TNF superfamily, and lymphotoxin alpha are ligands for herpesvirus entry mediator.
  Immunity, 8, 21-30.  
  9765392 G.Lu, Z.H.Zhou, M.L.Baker, J.Jakana, D.Cai, X.Wei, S.Chen, X.Gu, and W.Chiu (1998).
Structure of double-shelled rice dwarf virus.
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  9605317 J.Singh, E.Garber, H.Van Vlijmen, M.Karpusas, Y.M.Hsu, Z.Zheng, J.H.Naismith, and D.Thomas (1998).
The role of polar interactions in the molecular recognition of CD40L with its receptor CD40.
  Protein Sci, 7, 1124-1135.  
9512423 L.Shapiro, and P.E.Scherer (1998).
The crystal structure of a complement-1q family protein suggests an evolutionary link to tumor necrosis factor.
  Curr Biol, 8, 335-338.
PDB code: 1c28
9669810 T.A.Tran, B.V.Kallakury, R.A.Ambros, and J.S.Ross (1998).
Prognostic significance of tumor necrosis factors and their receptors in nonsmall cell lung carcinoma.
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Getting it together: signal transduction in G-protein coupled receptors by association of receptor domains.
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Proline-dependent oligomerization with arm exchange.
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Structure-based design and characterization of exocyclic peptidomimetics that inhibit TNF alpha binding to its receptor.
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Prediction of mutant activity and its application in molecular design of tumor necrosis factor-alpha.
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The TNF-ligand and receptor superfamilies: controllers of immunity and the Trojan horses of autoimmune disease?
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Molecular, structural, and biological characteristics of the tumor necrosis factor ligand superfamily.
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Human pro-tumor necrosis factor is a homotrimer.
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Structural changes of tumor necrosis factor alpha associated with membrane insertion and channel formation.
  Proc Natl Acad Sci U S A, 93, 1021-1026.  
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O-glycosylated species of natural human tumor-necrosis factor-alpha.
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Immune regulation by CD40 and its ligand GP39.
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Mapping protein-protein contact sites using cellulose-bound peptide scans.
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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
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Identification of two forms (31-33 and 48 kD) of the urinary soluble p55 tumor necrosis factor receptor that are differentially N- and O-glycosylated.
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Modeled structure of the 75-kDa neurotrophin receptor.
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Epitope mapping of monoclonal antibodies to tumor necrosis factor-alpha by synthetic peptide approach.
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2 A crystal structure of an extracellular fragment of human CD40 ligand.
  Structure, 3, 1031-1039.
PDB code: 1aly
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Functional discrepancies between tumor necrosis factor and lymphotoxin alpha explained by trimer stability and distinct receptor interactions.
  Eur J Immunol, 25, 2183-2189.  
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Expression of the functional soluble form of human fas ligand in activated lymphocytes.
  EMBO J, 14, 1129-1135.  
7635149 R.Hlodan, and R.H.Pain (1995).
The folding and assembly pathway of tumour necrosis factor TNF alpha, a globular trimeric protein.
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7531151 S.Hess, R.Kurrle, L.Lauffer, G.Riethmüller, and H.Engelmann (1995).
A cytotoxic CD40/p55 tumor necrosis factor receptor hybrid detects CD40 ligand on herpesvirus saimiri-transformed T cells.
  Eur J Immunol, 25, 80-86.  
8080166 B.Beutler, and C.Van Huffel (1994).
An evolutionary and functional approach to the TNF receptor/ligand family.
  Ann N Y Acad Sci, 730, 118-133.  
  7528588 D.Cosman (1994).
A family of ligands for the TNF receptor superfamily.
  Stem Cells, 12, 440-455.  
8024806 J.A.Wells (1994).
Structural and functional basis for hormone binding and receptor oligomerization.
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The TNF Receptors p55 and p75 Mediate Chemotaxis of PMN Induced by TNFalpha and a TNFalpha 36-62 Peptide.
  Mediators Inflamm, 3, 347-352.  
  8076595 P.R.Baum, R.B.Gayle, F.Ramsdell, S.Srinivasan, R.A.Sorensen, M.L.Watson, M.F.Seldin, E.Baker, G.R.Sutherland, and K.N.Clifford (1994).
Molecular characterization of murine and human OX40/OX40 ligand systems: identification of a human OX40 ligand as the HTLV-1-regulated protein gp34.
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7964492 T.J.Evans, D.Moyes, A.Carpenter, R.Martin, H.Loetscher, W.Lesslauer, and J.Cohen (1994).
Protective effect of 55- but not 75-kD soluble tumor necrosis factor receptor-immunoglobulin G fusion proteins in an animal model of gram-negative sepsis.
  J Exp Med, 180, 2173-2179.  
7511063 T.Takahashi, M.Tanaka, C.I.Brannan, N.A.Jenkins, N.G.Copeland, T.Suda, and S.Nagata (1994).
Generalized lymphoproliferative disease in mice, caused by a point mutation in the Fas ligand.
  Cell, 76, 969-976.  
7678782 A.Aruffo, M.Farrington, D.Hollenbaugh, X.Li, A.Milatovich, S.Nonoyama, J.Bajorath, L.S.Grosmaire, R.Stenkamp, and M.Neubauer (1993).
The CD40 ligand, gp39, is defective in activated T cells from patients with X-linked hyper-IgM syndrome.
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9137562 B.L.Kagan, T.Mirzabekov, D.Munoz, R.L.Baldwin, and B.Wisnieski (1993).
The role of channel formation in the mechanism of action of tumor necrosis factors.
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8391931 C.A.Smith, H.J.Gruss, T.Davis, D.Anderson, T.Farrah, E.Baker, G.R.Sutherland, C.I.Brannan, N.G.Copeland, and N.A.Jenkins (1993).
CD30 antigen, a marker for Hodgkin's lymphoma, is a receptor whose ligand defines an emerging family of cytokines with homology to TNF.
  Cell, 73, 1349-1360.  
8387891 D.W.Banner, A.D'Arcy, W.Janes, R.Gentz, H.J.Schoenfeld, C.Broger, H.Loetscher, and W.Lesslauer (1993).
Crystal structure of the soluble human 55 kd TNF receptor-human TNF beta complex: implications for TNF receptor activation.
  Cell, 73, 431-445.
PDB code: 1tnr
  7505680 J.Bajorath, R.Stenkamp, and A.Aruffo (1993).
Knowledge-based model building of proteins: concepts and examples.
  Protein Sci, 2, 1798-1810.
PDB code: 1kjd
8405064 R.G.Goodwin, W.S.Din, T.Davis-Smith, D.M.Anderson, S.D.Gimpel, T.A.Sato, C.R.Maliszewski, C.I.Brannan, N.G.Copeland, and N.A.Jenkins (1993).
Molecular cloning of a ligand for the inducible T cell gene 4-1BB: a member of an emerging family of cytokines with homology to tumor necrosis factor.
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8390056 R.S.Sidhu, and A.P.Bollon (1993).
Tumor necrosis factor activities and cancer therapy--a perspective.
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7505205 T.Suda, T.Takahashi, P.Golstein, and S.Nagata (1993).
Molecular cloning and expression of the Fas ligand, a novel member of the tumor necrosis factor family.
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8415875 Y.Mitsui, T.Senda, T.Shimazu, S.Matsuda, and J.Utsumi (1993).
Structural, functional and evolutionary implications of the three-dimensional crystal structure of murine interferon-beta.
  Pharmacol Ther, 58, 93.  
1607009 A.Brass, K.E.Kadler, J.T.Thomas, M.E.Grant, and R.P.Boot-Handford (1992).
The fibrillar collagens, collagen VIII, collagen X and the C1q complement proteins share a similar domain in their C-terminal non-collagenous regions.
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1310100 D.Aderka, H.Engelmann, Y.Maor, C.Brakebusch, and D.Wallach (1992).
Stabilization of the bioactivity of tumor necrosis factor by its soluble receptors.
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  1385114 D.Hollenbaugh, L.S.Grosmaire, C.D.Kullas, N.J.Chalupny, S.Braesch-Andersen, R.J.Noelle, I.Stamenkovic, J.A.Ledbetter, and A.Aruffo (1992).
The human T cell antigen gp39, a member of the TNF gene family, is a ligand for the CD40 receptor: expression of a soluble form of gp39 with B cell co-stimulatory activity.
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1331273 J.Rothe, G.Gehr, H.Loetscher, and W.Lesslauer (1992).
Tumor necrosis factor receptors--structure and function.
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1528078 M.D.Walkinshaw (1992).
Protein targets for structure-based drug design.
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1373060 R.H.Stiemer, U.Westenfelder, H.Gausepohl, M.Mirshahi, A.Gundt, R.W.Frank, and D.N.Männel (1992).
A common epitope on human tumor necrosis factor alpha and the autoantigen 'S-antigen/arrestin' induces TNF-alpha production.
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Three-dimensional crystal structure of recombinant murine interferon-beta.
  EMBO J, 11, 3193-3201.
PDB code: 1ifa
1660140 A.Ashkenazi, S.A.Marsters, D.J.Capon, S.M.Chamow, I.S.Figari, D.Pennica, D.V.Goeddel, M.A.Palladino, and D.H.Smith (1991).
Protection against endotoxic shock by a tumor necrosis factor receptor immunoadhesin.
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1786996 A.D.Nash, G.J.Barcham, M.R.Brandon, and A.E.Andrews (1991).
Molecular cloning, expression and characterization of ovine TNF alpha.
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1647190 B.B.Aggarwal (1991).
Structure of tumor necrosis factor and its receptor.
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1657606 G.Camussi, E.Albano, C.Tetta, and F.Bussolino (1991).
The molecular action of tumor necrosis factor-alpha.
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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
1742163 J.H.Riazance-Lawrence, A.Toumadje, and W.C.Johnson (1991).
The circular dichroism of tumor necrosis factor-alpha: measurement into the vacuum UV and analysis for secondary structure.
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Expression of genetically engineered immunoconjugates of lymphotoxin and a chimeric anti-ganglioside GD2 antibody.
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1649771 W.Fiers (1991).
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Localization of the active site of human tumour necrosis factor (hTNF) by mutational analysis.
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2258704 A.E.Postlethwaite, and J.M.Seyer (1990).
Stimulation of fibroblast chemotaxis by human recombinant tumor necrosis factor alpha (TNF-alpha) and a synthetic TNF-alpha 31-68 peptide.
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1702293 A.Himmler, I.Maurer-Fogy, M.Krönke, P.Scheurich, K.Pfizenmaier, M.Lantz, I.Olsson, R.Hauptmann, C.Stratowa, and G.R.Adolf (1990).
Molecular cloning and expression of human and rat tumor necrosis factor receptor chain (p60) and its soluble derivative, tumor necrosis factor-binding protein.
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2164226 P.Seckinger, J.H.Zhang, B.Hauptmann, and J.M.Dayer (1990).
Characterization of a tumor necrosis factor alpha (TNF-alpha) inhibitor: evidence of immunological cross-reactivity with the TNF receptor.
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2174582 S.R.Sprang (1990).
The divergent receptors for TNF.
  Trends Biochem Sci, 15, 366-368.  
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.