PDBsum entry 1ich

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Apoptosis PDB id
Protein chain
87 a.a. *
* Residue conservation analysis
PDB id:
Name: Apoptosis
Title: Solution structure of the tumor necrosis factor receptor-1 death domain
Structure: Tumor necrosis factor receptor-1. Chain: a. Fragment: death domain. Synonym: tnf-1. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 1 models
Authors: S.F.Sukits,L.-L.Lin,K.Malakian,R.Powers,G.-Y.Xu
Key ref:
S.F.Sukits et al. (2001). Solution structure of the tumor necrosis factor receptor-1 death domain. J Mol Biol, 310, 895-906. PubMed id: 11453696 DOI: 10.1006/jmbi.2001.4790
01-Apr-01     Release date:   01-Apr-02    
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Protein chain
Pfam   ArchSchema ?
P19438  (TNR1A_HUMAN) -  Tumor necrosis factor receptor superfamily member 1A
455 a.a.
87 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!
  Biological process     signal transduction   1 term 


DOI no: 10.1006/jmbi.2001.4790 J Mol Biol 310:895-906 (2001)
PubMed id: 11453696  
Solution structure of the tumor necrosis factor receptor-1 death domain.
S.F.Sukits, L.L.Lin, S.Hsu, K.Malakian, R.Powers, G.Y.Xu.
Tumor necrosis factor receptor-1 death domain (TNFR-1 DD) is the intracellular functional domain responsible for the receptor signaling activities. The solution structure of the R347K mutant of TNFR-1 DD was solved by NMR spectroscopy. A total of 20 structures were calculated by means of hybrid distance geometry-simulated annealing using a total of 1167 distance constraints and 117 torsion angle constraints. The atomic rms distribution about the mean coordinate positions for the 20 structures for residues composing the secondary structure region is 0.40 A for the backbone atoms and 1.09 A for all atoms. The structure consists of six antiparallel alpha-helices arranged in a similar fashion to the other members of the death domain superfamily. The secondary structure and three-dimensional structure of R347K TNFR1-DD are very similar to the secondary structure and deduced topology of the R347A TNFR1-DD mutant. Mutagenesis studies identified critical residues located in alpha2 and part of alpha3 and alpha4 that are crucial for self-interaction and interaction with TRADD. Structural superposition with previously solved proteins in the death domain superfamily reveals that the major differences between the structures reside in alpha2, alpha3, and alpha4. Interestingly, these regions correspond to the binding sites of TNFR1-DD, providing a structural basis for the specificity of death domain interactions and its subsequent signaling event.
  Selected figure(s)  
Figure 3.
Figure 3. Surface diagram of R347K TNFR-1 DD. The surface electrostatic potential in (a) and (b) is color-coded such that regions of the surface that are negatively charged are colored in red and regions that are positively charged are colored in blue. (c) and (d) Ribbon diagrams of the C a trace of the averaged minimized structure of R347K TNFR- 1 DD displaying the orientations depicted in (a) and (b), respectively. For clarity, a1, a5, and a6 are colored in red and a2, a3, and a4 are colored in green.
Figure 5.
Figure 5. (a) and (b) Surface diagrams displaying distinct orientations of R347K TNFR1-DD. Mutated residues that disrupt self-association and binding to TRADD DD 20 are colored blue in (a) and yellow in (b). (c) and (d) Ribbon dia- grams of the C a trace of the averaged minimized structure of R347K TNFR-1 DD displaying the orientations depicted in (a) and (b), respectively. In (c) and (d), the a-helical regions are colored red, the loop regions are colored gray, and the mutated residues that disrupt self-association and binding to TRADD DD are colored in blue and yellow.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 310, 895-906) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21207148 H.H.Park (2011).
Structural analyses of death domains and their interactions.
  Apoptosis, 16, 209-220.  
17922260 D.H.Tsao, W.T.Hum, S.Hsu, K.Malakian, and L.L.Lin (2007).
The NMR structure of the TRADD death domain, a key protein in the TNF signaling pathway.
  J Biomol NMR, 39, 337-342.  
17201679 H.H.Park, Y.C.Lo, S.C.Lin, L.Wang, J.K.Yang, and H.Wu (2007).
The death domain superfamily in intracellular signaling of apoptosis and inflammation.
  Annu Rev Immunol, 25, 561-586.  
17961823 T.L.Gururaja, S.Yung, R.Ding, J.Huang, X.Zhou, J.McLaughlin, S.Daniel-Issakani, R.Singh, R.D.Cooper, D.G.Payan, E.S.Masuda, and T.Kinoshita (2007).
A class of small molecules that inhibit TNFalpha-induced survival and death pathways via prevention of interactions between TNFalphaRI, TRADD, and RIP1.
  Chem Biol, 14, 1105-1118.  
16928684 M.Kukimoto-Niino, T.Takagi, R.Akasaka, K.Murayama, T.Uchikubo-Kamo, T.Terada, M.Inoue, S.Watanabe, A.Tanaka, Y.Hayashizaki, T.Kigawa, M.Shirouzu, and S.Yokoyama (2006).
Crystal structure of the RUN domain of the RAP2-interacting protein x.
  J Biol Chem, 281, 31843-31853.
PDB codes: 2cxf 2cxl 2dwg 2dwk
17139086 N.Handa, M.Kukimoto-Niino, R.Akasaka, K.Murayama, T.Terada, M.Inoue, T.Yabuki, M.Aoki, E.Seki, T.Matsuda, E.Nunokawa, A.Tanaka, Y.Hayashizaki, T.Kigawa, M.Shirouzu, and S.Yokoyama (2006).
Structure of the UNC5H2 death domain.
  Acta Crystallogr D Biol Crystallogr, 62, 1502-1509.
PDB code: 1wmg
16871532 S.L.Rebelo, S.E.Bainbridge, M.R.Amel-Kashipaz, P.M.Radford, R.J.Powell, I.Todd, and P.J.Tighe (2006).
Modeling of tumor necrosis factor receptor superfamily 1A mutants associated with tumor necrosis factor receptor-associated periodic syndrome indicates misfolding consistent with abnormal function.
  Arthritis Rheum, 54, 2674-2687.  
16006552 C.Sandu, E.Gavathiotis, T.Huang, I.Wegorzewska, and M.H.Werner (2005).
A mechanism for death receptor discrimination by death adaptors.
  J Biol Chem, 280, 31974-31980.  
14573612 J.M.Hill, G.Morisawa, T.Kim, T.Huang, Y.Wei, Y.Wei, and M.H.Werner (2004).
Identification of an expanded binding surface on the FADD death domain responsible for interaction with CD95/Fas.
  J Biol Chem, 279, 1474-1481.  
12576135 A.Clerk, S.M.Cole, T.E.Cullingford, J.G.Harrison, M.Jormakka, and D.M.Valks (2003).
Regulation of cardiac myocyte cell death.
  Pharmacol Ther, 97, 223-261.  
12604596 I.El Yazidi-Belkoura, E.Adriaenssens, L.Dollé, S.Descamps, and H.Hondermarck (2003).
Tumor necrosis factor receptor-associated death domain protein is involved in the neurotrophin receptor-mediated antiapoptotic activity of nerve growth factor in breast cancer cells.
  J Biol Chem, 278, 16952-16956.  
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.