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PR01919

Identifier
TNFACTORR1B  [View Relations]  [View Alignment]  
Accession
PR01919
No. of Motifs
5
Creation Date
28-APR-2008
Title
Tumour necrosis factor receptor 1B signature
Database References

PDB; 1CA9
SCOP; 1CA9
CATH; 1CA9
MIM; 191191
Literature References
1. ARMITAGE, R.
Tumor necrosis factor receptor superfamily members and their ligands.
CURR.OPIN.IMMUNOL. 6 407-413 (1994).
 
2. BANNER D., D'ARCY, A., JAMES, W., GENTZ, R., SCHOENFELD, H., BROGER, C.,
LOETSCHER, H. AND LESSLAUER, W.
Crystal structure of the soluble human 55 kD TNF receptor-human TNF-beta
complex: implications for TNF receptor activation.
CELL 73 431-445 (1993).
 
3. WU, H.
Assembly of post-receptor signaling complexes for the tumor necrosis factor
receptor superfamily.
ADV.PROTEIN CHEM. 68 225-279 (2004).
 
4. LOCKSLEY, R., KILLEEN, N. AND LENARDO, M.
The TNF and TNF Receptor Superfamilies: Integrating Mammalian Biology.
CELL 104 487-501 (2001).
 
5. GRAVESTEIN, L. AND BORST, J.
Tumor necrosis factor receptor family members in the immune system.
SEMIN.IMMUNOL. 10 423-434 (1998).
 
6. LOENEN, W.
D27 and (TNFR) relatives in the immune system: their role in health and
disease.
SEMIN.IMMUNOL. 10 417-422 (1998).
 
7. BELTINGER, C., WHITE, P., MARIS, J., SULMAN, E., JENSEN, S.,
LEPASLIER, D., STALLARD, B., GOEDDEL, D., DE SAUVAGE, F. AND BRODEUR, G.
Physical mapping and genomic structure of the human TNFR2 gene.
GENOMICS 35 94-100 (1996).

Documentation
The tumour necrosis factor (TNF) receptor (TNFR) superfamily comprises more
than 20 type-I transmembrane proteins. Family members are defined based on
similarity in their extracellular domain - a region that contains many
cysteine residues arranged in a specific repetitive pattern [1]. The
cysteines allow formation of an extended rod-like structure, responsible for
ligand binding [2].
 
Upon receptor activation, different intracellular signalling complexes are
assembled for different members of the TNFR superfamily, depending on their
intracellular domains and sequences [3]. Activation of TNFRs can therefore
induce a range of disparate effects, including cell proliferation,
differentiation, survival, or apoptotic cell death, depending upon the
receptor involved [4,5].
 
TNFRs are widely distributed and play important roles in many crucial
biological processes, such as lymphoid and neuronal development, innate and
adaptive immunity, and maintenance of cellular homeostasis [3]. Drugs that
manipulate their signalling have potential roles in the prevention and
treatment of many diseases, such as viral infections, coronary heart
disease, transplant rejection, and immune disease [6].
 
TNF receptor 1B (also known as TNF-R2 and CD120b antigen) is present on many
cell types, especially those of myeloid origin, and is strongly expressed on
stimulated T and B lymphocytes. It is the main TNF receptor found on
circulating T cells and is the major mediator of autoregulatory apoptosis in
CD8+ cells [7].
 
TNFACTORR1B is a 5-element fingerprint that provides a signature for tumour
necrosis factor receptor 1B. The fingerprint was derived from an initial
alignment of 2 sequences: the motifs were drawn from conserved regions
either side of the transmembrane domain, focusing on those areas that
characterise TNF receptor 1B but distinguish it from other TNF receptor
subtypes - motif 1 resides within the extracellular N-terminal region; and 
motifs 2-5 lie within the intracellular C-terminal portion of the alignment.
Two iterations on SPTR55_38f were required to reach convergence, at which
point a true set comprising 9 sequences was identified.
Summary Information
9 codes involving  5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
599999
400000
300000
200000
12345
True Positives
A1YPR7_PIG    A7Y2G6_PIG    A7Y2G9_PIG    Q3MHI9_BOVIN  
Q3U2A9_MOUSE Q545P4_MOUSE TNR1B_HUMAN TNR1B_MOUSE
TNR1B_RAT
Sequence Titles
A1YPR7_PIG  Tumor necrosis factor receptor 2 - Sus scrofa (Pig). 
A7Y2G6_PIG Tumor necrosis factor receptor 2 - Sus scrofa (Pig).
A7Y2G9_PIG Tumor necrosis factor receptor 2 isoform - Sus scrofa (Pig).
Q3MHI9_BOVIN Tumor necrosis factor receptor superfamily, member 1B - Bos taurus (Bovine).
Q3U2A9_MOUSE NOD-derived CD11c +ve dendritic cells cDNA, RIKEN full-length enriched library, clone:F630223G21 product:tumor necrosis factor receptor superfamily, member 1b, full insert sequence - Mus musculus (Mouse).
Q545P4_MOUSE Adult male liver cDNA, RIKEN full-length enriched library, clone:1300002A12 product:tumor necrosis factor receptor superfamily, member 1b, full insert sequence (Bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830136B10 product:tumor necrosis factor receptor superfamily, member 1b, full insert sequence) (4 days neonate male adipose cDNA, RIKEN full-length enriched library, clone:B430202I20 product:tumor necrosis factor receptor superfamily, member 1b, full insert sequence) (Adult male lung cDNA, RIKEN full- length enriched library, clone:1200014B20 product:tumor necrosis factor receptor superfamily, member 1b, full insert sequence) - Mus musculus (Mouse).
TNR1B_HUMAN Tumor necrosis factor receptor superfamily member 1B precursor (Tumor necrosis factor receptor 2) (TNF-R2) (Tumor necrosis factor receptor type II) (p75) (p80 TNF-alpha receptor) (CD120b antigen) (Etanercept) [Contains: Tumor necrosis factor receptor superfamily member 1b, membrane form; Tumor necrosis factor-binding protein 2 (TBPII) (TBP- 2)] - Homo sapiens (Human).
TNR1B_MOUSE Tumor necrosis factor receptor superfamily member 1B precursor (Tumor necrosis factor receptor 2) (TNF-R2) (Tumor necrosis factor receptor type II) (p75) (p80 TNF-alpha receptor) - Mus musculus (Mouse).
TNR1B_RAT Tumor necrosis factor receptor superfamily member 1B precursor (Tumor necrosis factor receptor 2) (TNF-R2) (Tumor necrosis factor receptor type II) (p75) (p80 TNF-alpha receptor) - Rattus norvegicus (Rat).
Scan History
SPTR55_38f 2  300  NSINGLE    
Initial Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
ICSILAIPGNAS TNR1B_MOUSE 186 186 -
ICNVVAIPGNAS TNR1B_HUMAN 184 184 -

Motif 2 width=14
Element Seqn Id St Int Rpt
KPSCLQRDAKVPHV TNR1B_MOUSE 291 93 -
KPLCLQREAKVPHL TNR1B_HUMAN 290 94 -

Motif 3 width=19
Element Seqn Id St Int Rpt
EKSQDAVGLEQQHLLTTAP TNR1B_MOUSE 307 2 -
DKARGTQGPEQQHLLITAP TNR1B_HUMAN 306 2 -

Motif 4 width=15
Element Seqn Id St Int Rpt
HGTHVNVTCIVNVCS TNR1B_MOUSE 377 51 -
HGTQVNVTCIVNVCS TNR1B_HUMAN 375 50 -

Motif 5 width=20
Element Seqn Id St Int Rpt
VGDPDAKPSASPKDEQVPFS TNR1B_MOUSE 407 15 -
MGDTDSSPSESPKDEQVPFS TNR1B_HUMAN 405 15 -
Final Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
ICSILAIPGNAS Q3U2A9_MOUSE 186 186 -
ICSILAIPGNAS TNR1B_MOUSE 186 186 -
ICNVVAIPGNAS TNR1B_HUMAN 184 184 -
ICSILAIPGNAS Q545P4_MOUSE 186 186 -
ICSILAIPGNAS TNR1B_RAT 186 186 -
ICSSVAIPGTAR A7Y2G6_PIG 186 186 -
ICSSVAIPGTAR A7Y2G9_PIG 136 136 -
ICSSVAIPGTAR A1YPR7_PIG 133 133 -
NCSSVAIPGTAS Q3MHI9_BOVIN 184 184 -

Motif 2 width=14
Element Seqn Id St Int Rpt
KPSCLQRDAKVPHV Q3U2A9_MOUSE 291 93 -
KPSCLQRDAKVPHV TNR1B_MOUSE 291 93 -
KPLCLQREAKVPHL TNR1B_HUMAN 290 94 -
KPSCLQRDAKVPHV Q545P4_MOUSE 291 93 -
KPSCLQRETMVPHL TNR1B_RAT 291 93 -
KPFCLQGDAKVPHL A7Y2G6_PIG 290 92 -
KPFCLQGDAKVPHL A7Y2G9_PIG 240 92 -
KPFCLQGDAKVPHL A1YPR7_PIG 237 92 -
KPFCLQGDAKVPHL Q3MHI9_BOVIN 288 92 -

Motif 3 width=19
Element Seqn Id St Int Rpt
EKSQDAVGLEQQHLLTTAP Q3U2A9_MOUSE 307 2 -
EKSQDAVGLEQQHLLTTAP TNR1B_MOUSE 307 2 -
DKARGTQGPEQQHLLITAP TNR1B_HUMAN 306 2 -
EKSQDAVGLEQQHLLTTAP Q545P4_MOUSE 307 2 -
DKSQDAIGLEQQHLLTTAP TNR1B_RAT 307 2 -
KKARSVPGPEQQHLLTTAP A7Y2G6_PIG 306 2 -
KKARSVPGPEQQHLLTTAP A7Y2G9_PIG 256 2 -
EKARSVPGPEQQHLLTTAP A1YPR7_PIG 253 2 -
NKAQGAPGPEQQHLLTTAP Q3MHI9_BOVIN 304 2 -

Motif 4 width=15
Element Seqn Id St Int Rpt
HGTHVNVTCIVNVCS Q3U2A9_MOUSE 377 51 -
HGTHVNVTCIVNVCS TNR1B_MOUSE 377 51 -
HGTQVNVTCIVNVCS TNR1B_HUMAN 375 50 -
HGTHVNVTCIVNVCS Q545P4_MOUSE 377 51 -
HGTHVNVTCIVNVCS TNR1B_RAT 377 51 -
HGTQVNVTCIVNVCS A7Y2G6_PIG 376 51 -
HGTQVNVTCIVNVCS A7Y2G9_PIG 326 51 -
HGTQVNVTCIVNVCS A1YPR7_PIG 323 51 -
HGTQVNVTCIVNVCS Q3MHI9_BOVIN 374 51 -

Motif 5 width=20
Element Seqn Id St Int Rpt
VGDPDAKPSASPKDEQVPFS Q3U2A9_MOUSE 407 15 -
VGDPDAKPSASPKDEQVPFS TNR1B_MOUSE 407 15 -
MGDTDSSPSESPKDEQVPFS TNR1B_HUMAN 405 15 -
VGDPDAKPSASPKDEQVPFS Q545P4_MOUSE 407 15 -
VGDPDANPSGSPKDEQVPFS TNR1B_RAT 407 15 -
TRDTDASPSSSPKDEQVPFS A7Y2G6_PIG 405 14 -
TRDTDASPSSSPKDEQVPFS A7Y2G9_PIG 355 14 -
TRDTDASPSSSPKDEQVPCR A1YPR7_PIG 352 14 -
TRDTDASTPNSPKEEQVPFS Q3MHI9_BOVIN 403 14 -