PDBsum entry 1d4v

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Apoptosis PDB id
Protein chains
163 a.a. *
117 a.a. *
Waters ×154
* Residue conservation analysis
PDB id:
Name: Apoptosis
Title: Crystal structure of trail-dr5 complex
Structure: Tnf-related apoptosis inducing ligand. Chain: b. Fragment: single subunit. Synonym: trail. Engineered: yes. Death receptor 5. Chain: a. Fragment: extracellular region. Synonym: dr5.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: transient expression as ig fusion protein. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell: 293t cells
Biol. unit: Hexamer (from PDB file)
2.20Å     R-factor:   0.221     R-free:   0.270
Authors: J.Mongkolsapaya,J.M.Grimes,D.I.Stuart,E.Y.Jones,G.R.Screaton
Key ref:
J.Mongkolsapaya et al. (1999). Structure of the TRAIL-DR5 complex reveals mechanisms conferring specificity in apoptotic initiation. Nat Struct Biol, 6, 1048-1053. PubMed id: 10542098 DOI: 10.1038/14935
06-Oct-99     Release date:   01-Nov-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P50591  (TNF10_HUMAN) -  Tumor necrosis factor ligand superfamily member 10
281 a.a.
163 a.a.
Protein chain
Pfam   ArchSchema ?
O14763  (TR10B_HUMAN) -  Tumor necrosis factor receptor superfamily member 10B
440 a.a.
117 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     TRAIL binding     2 terms  


DOI no: 10.1038/14935 Nat Struct Biol 6:1048-1053 (1999)
PubMed id: 10542098  
Structure of the TRAIL-DR5 complex reveals mechanisms conferring specificity in apoptotic initiation.
J.Mongkolsapaya, J.M.Grimes, N.Chen, X.N.Xu, D.I.Stuart, E.Y.Jones, G.R.Screaton.
TRAIL, an apoptosis inducing ligand, has at least four cell surface receptors including the death receptor DR5. Here we report the crystal structure at 2.2 A resolution of a complex between TRAIL and the extracellular region of DR5. TRAIL forms a central homotrimer around which three DR5 molecules bind. Radical differences in the surface charge of the ligand, together with variation in the alignment of the two receptor domains confer specificity between members of these ligand and receptor families. The existence of a switch mechanism allowing variation in receptor domain alignment may mean that it is possible to engineer receptors with multiple specificities by exploiting contact positions unique to individual receptor-ligand pairs.
  Selected figure(s)  
Figure 1.
Figure 1. The structure of TRAIL, DR5 and the TRAIL−DR5 complex. a, Stereo view of the complex. The three crystallographically equivalent copies of the TRAIL subunit (yellow, cyan, pink) and DR5 (blue, green, red) are depicted schematically and the TRAIL trimer is enclosed in a transparent molecular envelope. This orientation defines a standard view. b, The complex as depicted in (a) but viewed down the three-fold axis. The orientation is such that the cell surface presenting DR5 is above the page and that for TRAIL is below the page. c, Superposition of TRAIL (pink) with TNF (blue). The secondary structure elements for TRAIL are also marked on the sequence alignment in Fig. 2a. The r.m.s. deviation is 0.9 Å for 120 structurally equivalent C atoms. The major extension of the AA" loop in TRAIL is highlighted by yellow stripes. The cell surface position is not to scale. d, Comparison of DR5 and TNF-R1. DR5 and TNF-R1 (from the TNF −TNF-R1 complex) are depicted schematically in the left and right panels respectively with equivalent regions in identical colors. The central panel is based on superposition of DR5 D1 and TNF-R1 D2. The schematic representation of TNF-R1 is shown in gray while that of DR5 is in green. Disulfide bonds are depicted in yellow as ball-and-stick representation. e, Portion of the final 2F[o] - F[c] electron density map contoured at 1 , showing a portion of the TRAIL structure in the BC loop.
Figure 3.
Figure 3. Elements of conservation and specificity in ligand−receptor binding. a, Conservation in ligand-receptor interactions. Close up of the interaction involving the B1 (cyan) surfaces in the TRAIL−DR5 and TNF −TNF-R1 complexes centered on the key tyrosine residue (Tyr 216 in TRAIL). In this and in (c), the polypeptide chains are represented schematically as in Fig. 1a and the solvent-accessible surfaces of the receptors (calculated in isolation) are shown as semi-transparent envelopes. b, Comparison of surface charge between TRAIL, TNF , TNF and their receptors. Blue denotes positive, and red negative; electrostatic potential is contoured at 8.0 kT in program GRASP^31. The views of ligand and receptor are as in Fig. 2b. c, Interaction of Arg 149 in the AA" loop of TRAIL with Glu 147 in DR5. d, BIAcore analysis showing binding of DR5 to wild type TRAIL or the mutant lacking the AA" loop. e, Immunoprecipitation with DR5-Fc in the presence of wild type (W) or the slightly smaller AA" TRAIL mutant (M). Lanes 1 and 2 immunoprecipitated material (IP), lanes 3 and 4 material left in supernatant (SN) following immunoprecipitation.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 1048-1053) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21300979 K.Hanada, Q.J.Wang, T.Inozume, and J.C.Yang (2011).
Molecular identification of an MHC-independent ligand recognized by a human {alpha}/{beta} T-cell receptor.
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21368856 C.R.Reis, A.M.van der Sloot, A.Natoni, E.Szegezdi, R.Setroikromo, M.Meijer, K.Sjollema, F.Stricher, R.H.Cool, A.Samali, L.Serrano, and W.J.Quax (2010).
Rapid and efficient cancer cell killing mediated by high-affinity death receptor homotrimerizing TRAIL variants.
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20531300 F.Gonzalvez, and A.Ashkenazi (2010).
New insights into apoptosis signaling by Apo2L/TRAIL.
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21059944 H.M.Ta, G.T.Nguyen, H.M.Jin, J.Choi, H.Park, N.Kim, H.Y.Hwang, and K.K.Kim (2010).
Structure-based development of a receptor activator of nuclear factor-kappaB ligand (RANKL) inhibitor peptide and molecular basis for osteopetrosis.
  Proc Natl Acad Sci U S A, 107, 20281-20286.
PDB codes: 3nzy 3qbq
20156289 J.Vrielink, M.S.Heins, R.Setroikromo, E.Szegezdi, M.M.Mullally, A.Samali, and W.J.Quax (2010).
Synthetic constrained peptide selectively binds and antagonizes death receptor 5.
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The extracellular matrix glycoprotein elastin microfibril interface located protein 2: a dual role in the tumor microenvironment.
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19522538 C.Zhan, Q.Yan, Y.Patskovsky, Z.Li, R.Toro, A.Meyer, H.Cheng, M.Brenowitz, S.G.Nathenson, and S.C.Almo (2009).
Biochemical and structural characterization of the human TL1A ectodomain.
  Biochemistry, 48, 7636-7645.
PDB codes: 2qe3 2rjk 2rjl
19509255 D.V.Rozanov, A.Y.Savinov, V.S.Golubkov, O.L.Rozanova, T.I.Postnova, E.A.Sergienko, S.Vasile, A.E.Aleshin, M.F.Rega, M.Pellecchia, and A.Y.Strongin (2009).
Engineering a leucine zipper-TRAIL homotrimer with improved cytotoxicity in tumor cells.
  Mol Cancer Ther, 8, 1515-1525.  
19637313 E.Oikonomou, V.Kosmidou, A.Katseli, K.Kothonidis, D.Mourtzoukou, G.Kontogeorgos, L.Andera, G.Zografos, and A.Pintzas (2009).
TRAIL receptor upregulation and the implication of KRAS/BRAF mutations in human colon cancer tumors.
  Int J Cancer, 125, 2127-2135.  
19241374 F.He, W.Dang, K.Saito, S.Watanabe, N.Kobayashi, P.Güntert, T.Kigawa, A.Tanaka, Y.Muto, and S.Yokoyama (2009).
Solution structure of the cysteine-rich domain in Fn14, a member of the tumor necrosis factor receptor superfamily.
  Protein Sci, 18, 650-656.
PDB code: 2rpj
19426226 G.Cai, and G.J.Freeman (2009).
The CD160, BTLA, LIGHT/HVEM pathway: a bidirectional switch regulating T-cell activation.
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19758994 M.Baud'huin, L.Duplomb, S.Téletchéa, C.Charrier, M.Maillasson, M.Fouassier, and D.Heymann (2009).
Factor VIII-von Willebrand factor complex inhibits osteoclastogenesis and controls cell survival.
  J Biol Chem, 284, 31704-31713.  
19194800 T.Newsom-Davis, S.Prieske, and H.Walczak (2009).
Is TRAIL the holy grail of cancer therapy?
  Apoptosis, 14, 607-623.  
18219321 C.Adams, K.Totpal, D.Lawrence, S.Marsters, R.Pitti, S.Yee, S.Ross, L.Deforge, H.Koeppen, M.Sagolla, D.Compaan, H.Lowman, S.Hymowitz, and A.Ashkenazi (2008).
Structural and functional analysis of the interaction between the agonistic monoclonal antibody Apomab and the proapoptotic receptor DR5.
  Cell Death Differ, 15, 751-761.
PDB code: 4od2
17671978 T.A.Wassenaar, W.J.Quax, and A.E.Mark (2008).
The conformation of the extracellular binding domain of Death Receptor 5 in the presence and absence of the activating ligand TRAIL: a molecular dynamics study.
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18474604 V.Tur, A.M.van der Sloot, C.R.Reis, E.Szegezdi, R.H.Cool, A.Samali, L.Serrano, and W.J.Quax (2008).
DR4-selective tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) variants obtained by structure-based design.
  J Biol Chem, 283, 20560-20568.  
17551494 E.Oikonomou, K.Kothonidis, E.Taoufik, E.Probert, G.Zografos, G.Nasioulas, L.Andera, and A.Pintzas (2007).
Newly established tumourigenic primary human colon cancer cell lines are sensitive to TRAIL-induced apoptosis in vitro and in vivo.
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17449269 F.K.Chan (2007).
Three is better than one: pre-ligand receptor assembly in the regulation of TNF receptor signaling.
  Cytokine, 37, 101-107.  
16731632 A.M.van der Sloot, V.Tur, E.Szegezdi, M.M.Mullally, R.H.Cool, A.Samali, L.Serrano, and W.J.Quax (2006).
Designed tumor necrosis factor-related apoptosis-inducing ligand variants initiating apoptosis exclusively via the DR5 receptor.
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16710361 C.Sandu, G.Morisawa, I.Wegorzewska, T.Huang, A.F.Arechiga, J.M.Hill, T.Kim, C.M.Walsh, and M.H.Werner (2006).
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16905106 D.M.Compaan, and S.G.Hymowitz (2006).
The crystal structure of the costimulatory OX40-OX40L complex.
  Structure, 14, 1321-1330.
PDB codes: 2hev 2hew 2hey
16144019 J.Yoo, S.Choi, K.S.Hwang, W.K.Cho, C.R.Jung, S.T.Kwon, and D.S.Im (2006).
Adeno-associated virus-mediated gene transfer of a secreted form of TRAIL inhibits tumor growth and occurrence in an experimental tumor model.
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16680194 K.Aoki, H.Saito, C.Itzstein, M.Ishiguro, T.Shibata, R.Blanque, A.H.Mian, M.Takahashi, Y.Suzuki, M.Yoshimatsu, A.Yamaguchi, P.Deprez, P.Mollat, R.Murali, K.Ohya, W.C.Horne, and R.Baron (2006).
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16528386 T.O.Garnett, M.Filippova, and P.J.Duerksen-Hughes (2006).
Accelerated degradation of FADD and procaspase 8 in cells expressing human papilloma virus 16 E6 impairs TRAIL-mediated apoptosis.
  Cell Death Differ, 13, 1915-1926.  
  16887991 Y.Huang, N.Erdmann, H.Peng, S.Herek, J.S.Davis, X.Luo, T.Ikezu, and J.Zheng (2006).
TRAIL-mediated apoptosis in HIV-1-infected macrophages is dependent on the inhibition of Akt-1 phosphorylation.
  J Immunol, 177, 2304-2313.  
16767747 Y.Jiang, K.Chen, Z.Tang, Z.Zeng, W.Yao, D.Sun, W.Ka, D.He, Z.Wen, and S.Chien (2006).
TRAIL gene reorganizes the cytoskeleton and decreases the motility of human leukemic Jurkat cells.
  Cell Motil Cytoskeleton, 63, 471-482.  
16169851 D.M.Compaan, L.C.Gonzalez, I.Tom, K.M.Loyet, D.Eaton, and S.G.Hymowitz (2005).
Attenuating lymphocyte activity: the crystal structure of the BTLA-HVEM complex.
  J Biol Chem, 280, 39553-39561.
PDB code: 2aw2
16319225 L.Clancy, K.Mruk, K.Archer, M.Woelfel, J.Mongkolsapaya, G.Screaton, M.J.Lenardo, and F.K.Chan (2005).
Preligand assembly domain-mediated ligand-independent association between TRAIL receptor 4 (TR4) and TR2 regulates TRAIL-induced apoptosis.
  Proc Natl Acad Sci U S A, 102, 18099-18104.  
16212486 N.Yan, and Y.Shi (2005).
Mechanisms of apoptosis through structural biology.
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15987601 R.A.Daniels, H.Turley, F.C.Kimberley, X.S.Liu, J.Mongkolsapaya, P.Ch'En, X.N.Xu, B.Q.Jin, F.Pezzella, and G.R.Screaton (2005).
Expression of TRAIL and TRAIL receptors in normal and malignant tissues.
  Cell Res, 15, 430-438.  
15520016 R.F.Kelley, K.Totpal, S.H.Lindstrom, M.Mathieu, K.Billeci, L.Deforge, R.Pai, S.G.Hymowitz, and A.Ashkenazi (2005).
Receptor-selective mutants of apoptosis-inducing ligand 2/tumor necrosis factor-related apoptosis-inducing ligand reveal a greater contribution of death receptor (DR) 5 than DR4 to apoptosis signaling.
  J Biol Chem, 280, 2205-2212.  
15711921 S.Bouralexis, D.M.Findlay, and A.Evdokiou (2005).
Death to the bad guys: targeting cancer via Apo2L/TRAIL.
  Apoptosis, 10, 35-51.  
15542592 S.G.Hymowitz, D.R.Patel, H.J.Wallweber, S.Runyon, M.Yan, J.Yin, S.K.Shriver, N.C.Gordon, B.Pan, N.J.Skelton, R.F.Kelley, and M.A.Starovasnik (2005).
Structures of APRIL-receptor complexes: like BCMA, TACI employs only a single cysteine-rich domain for high affinity ligand binding.
  J Biol Chem, 280, 7218-7227.
PDB codes: 1xu1 1xu2 1xut
16239906 S.W.Fesik (2005).
Promoting apoptosis as a strategy for cancer drug discovery.
  Nat Rev Cancer, 5, 876-885.  
15093829 G.Zhang (2004).
Tumor necrosis factor family ligand-receptor binding.
  Curr Opin Struct Biol, 14, 154-160.  
15158769 S.Shankar, and R.K.Srivastava (2004).
Enhancement of therapeutic potential of TRAIL by cancer chemotherapy and irradiation: mechanisms and clinical implications.
  Drug Resist Updat, 7, 139-156.  
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.
  Nucleic Acids Res, 32, 6120-6128.  
12787570 A.Almasan, and A.Ashkenazi (2003).
Apo2L/TRAIL: apoptosis signaling, biology, and potential for cancer therapy.
  Cytokine Growth Factor Rev, 14, 337-348.  
12715002 H.M.Kim, K.S.Yu, M.E.Lee, D.R.Shin, Y.S.Kim, S.G.Paik, O.J.Yoo, H.Lee, and J.O.Lee (2003).
Crystal structure of the BAFF-BAFF-R complex and its implications for receptor activation.
  Nat Struct Biol, 10, 342-348.
PDB codes: 1otz 1p0t
12485619 H.Wajant, K.Pfizenmaier, and P.Scheurich (2003).
Non-apoptotic Fas signaling.
  Cytokine Growth Factor Rev, 14, 53-66.  
12654257 N.Ozören, and W.S.El-Deiry (2003).
Cell surface Death Receptor signaling in normal and cancer cells.
  Semin Cancer Biol, 13, 135-147.  
12466268 P.Schneider, D.Olson, A.Tardivel, B.Browning, A.Lugovskoy, D.Gong, M.Dobles, S.Hertig, K.Hofmann, H.Van Vlijmen, Y.M.Hsu, L.C.Burkly, J.Tschopp, and T.S.Zheng (2003).
Identification of a new murine tumor necrosis factor receptor locus that contains two novel murine receptors for tumor necrosis factor-related apoptosis-inducing ligand (TRAIL).
  J Biol Chem, 278, 5444-5454.  
14656435 S.G.Hymowitz, D.M.Compaan, M.Yan, H.J.Wallweber, V.M.Dixit, M.A.Starovasnik, and Vos (2003).
The crystal structures of EDA-A1 and EDA-A2: splice variants with distinct receptor specificity.
  Structure, 11, 1513-1520.
PDB codes: 1rj7 1rj8
12831538 X.S.Liu, Y.Zhu, W.N.Han, Y.N.Li, L.H.Chen, W.Jia, C.J.Song, F.Liu, K.Yang, Q.Li, and B.Q.Jin (2003).
Preparation and characterization of a set of monoclonal antibodies to TRAIL and TRAIL receptors DR4, DR5, DcR1, and DcR2.
  Hybrid Hybridomics, 22, 121-125.  
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
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.  
11754357 P.G.Hargreaves, and A.Al-Shamkhani (2002).
Soluble CD30 binds to CD153 with high affinity and blocks transmembrane signaling by CD30.
  Eur J Immunol, 32, 163-173.  
11733492 S.Ito, K.Wakabayashi, O.Ubukata, S.Hayashi, F.Okada, and T.Hata (2002).
Crystal structure of the extracellular domain of mouse RANK ligand at 2.2-A resolution.
  J Biol Chem, 277, 6631-6636.
PDB code: 1iqa
11309507 A.K.Simon, O.Williams, J.Mongkolsapaya, B.Jin, X.N.Xu, H.Walczak, and G.R.Screaton (2001).
Tumor necrosis factor-related apoptosis-inducing ligand in T cell development: sensitivity of human thymocytes.
  Proc Natl Acad Sci U S A, 98, 5158-5163.  
11562359 B.G.Werneburg, S.J.Zoog, T.T.Dang, M.R.Kehry, and J.J.Crute (2001).
Molecular characterization of CD40 signaling intermediates.
  J Biol Chem, 276, 43334-43342.  
  11581298 J.Lam, C.A.Nelson, F.P.Ross, S.L.Teitelbaum, and D.H.Fremont (2001).
Crystal structure of the TRANCE/RANKL cytokine reveals determinants of receptor-ligand specificity.
  J Clin Invest, 108, 971-979.
PDB code: 1jtz
11574464 S.G.Hymowitz, E.H.Filvaroff, J.P.Yin, J.Lee, L.Cai, P.Risser, M.Maruoka, W.Mao, J.Foster, R.F.Kelley, G.Pan, A.L.Gurney, Vos, and M.A.Starovasnik (2001).
IL-17s adopt a cystine knot fold: structure and activity of a novel cytokine, IL-17F, and implications for receptor binding.
  EMBO J, 20, 5332-5341.
PDB code: 1jpy
11828422 U.Sartorius, I.Schmitz, and P.H.Krammer (2001).
Molecular mechanisms of death-receptor-mediated apoptosis.
  Chembiochem, 2, 20-29.  
11114500 E.Y.Jones (2000).
The tumour necrosis factor receptor family: life or death choices.
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10894161 F.C.Kischkel, D.A.Lawrence, A.Chuntharapai, P.Schow, K.J.Kim, and A.Ashkenazi (2000).
Apo2L/TRAIL-dependent recruitment of endogenous FADD and caspase-8 to death receptors 4 and 5.
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11053089 F.K.Chan (2000).
The pre-ligand binding assembly domain: a potential target of inhibition of tumour necrosis factor receptor function.
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11015187 F.P.Ottensmeyer, D.R.Beniac, R.Z.Luo, and C.C.Yip (2000).
Mechanism of transmembrane signaling: insulin binding and the insulin receptor.
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10781406 G.Screaton, and X.N.Xu (2000).
T cell life and death signalling via TNF-receptor family members.
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10891884 H.T.Idriss, and J.H.Naismith (2000).
TNF alpha and the TNF receptor superfamily: structure-function relationship(s).
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10880534 J.S.Thompson, P.Schneider, S.L.Kalled, L.Wang, E.A.Lefevre, T.G.Cachero, F.MacKay, S.A.Bixler, M.Zafari, Z.Y.Liu, S.A.Woodcock, F.Qian, M.Batten, C.Madry, Y.Richard, C.D.Benjamin, J.L.Browning, A.Tsapis, J.Tschopp, and C.Ambrose (2000).
BAFF binds to the tumor necrosis factor receptor-like molecule B cell maturation antigen and is important for maintaining the peripheral B cell population.
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10753817 M.C.Deller, and E.Yvonne Jones (2000).
Cell surface receptors.
  Curr Opin Struct Biol, 10, 213-219.  
10997905 M.C.Deller, K.R.Hudson, S.Ikemizu, J.Bravo, E.Y.Jones, and J.K.Heath (2000).
Crystal structure and functional dissection of the cytostatic cytokine oncostatin M.
  Structure, 8, 863-874.
PDB code: 1evs
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
11057900 S.W.Fesik (2000).
Insights into programmed cell death through structural biology.
  Cell, 103, 273-282.  
10958661 Y.Lin, A.Devin, A.Cook, M.M.Keane, M.Kelliher, S.Lipkowitz, and Z.G.Liu (2000).
The death domain kinase RIP is essential for TRAIL (Apo2L)-induced activation of IkappaB kinase and c-Jun N-terminal kinase.
  Mol Cell Biol, 20, 6638-6645.  
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.