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PR01964

Identifier
TNFACTORR13C  [View Relations]  [View Alignment]  
Accession
PR01964
No. of Motifs
3
Creation Date
23-JUN-2009
Title
Tumour necrosis factor receptor 13C signature
Database References

PFAM; PF09256 BaffR-Tall_bind
INTERPRO; IPR015336
PDB; 1OQE; 1OSX; 1P0T; 2HFG
SCOP; 1OQE; 1OSX; 1P0T; 2HFG
CATH; 1OQE; 1OSX; 1P0T; 2HFG
MIM; 606269
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. THOMPSON, J., BIXLER, S., QIAN, F., VORA, K., SCOTT, M., CACHERO, T., 
HESSION, C., SCHNEIDER, P., SIZING, I., MULLEN, C., STRAUCH, K., ZAFARI, M.,
BENJAMIN, C., TSCHOPP, J., BROWNING, J. AND AMBROSE, C.
BAFF-R, a newly identified TNF receptor that specifically interacts with 
BAFF.
SCIENCE 293 2108-2111 (2001).
 
8. JU, Z., SHI, G., ZUO, J., ZHANG, J. AND JIAN, S.
Unexpected development of autoimmunity in BAFF-R-mutant MRL-lpr mice.
IMMUNOLOGY 120 281-289 (2007). 

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 13C is also known as B-cell activating factor (BAFF) receptor 
[7]. It appears to be the principal receptor in mediating BAFF-dependent 
B-cell signalling, and plays a critical role in late-stage B-cell maturation
and survival [8].
 
TNFACTORR13C is a 3-element fingerprint that provides a signature for tumour
necrosis factor receptor 13C. The fingerprint was derived from an initial
alignment of 3 sequences: the motifs were drawn from conserved regions 
spanning virtually the full alignment length, focusing on those sections 
that characterise TNF receptor 13C but distinguish it from other TNF 
receptor subtypes - motif 1 lies in the extracellular N-terminal region;
motif 2 spans part of the extracellular N-terminal region and part of the 
transmembrane domain; and motif 3 resides within the intracellular 
C-terminal region. Two iterations on SPTR57_40f were required to reach 
convergence, at which point a true set comprising 8 sequences was 
identified.
Summary Information
8 codes involving  3 elements
0 codes involving 2 elements
Composite Feature Index
3888
2000
123
True Positives
Q3BK46_CHICK  Q3SXS6_MOUSE  Q3SXS7_MOUSE  Q3U106_MOUSE  
Q5H8V1_HUMAN Q8R4W8_MOUSE TR13C_HUMAN TR13C_MOUSE
Sequence Titles
Q3BK46_CHICK Tumor necrosis factor receptor superfamily, member 13c - Gallus gallus (Chicken). 
Q3SXS6_MOUSE BAFF receptor - Mus musculus (Mouse).
Q3SXS7_MOUSE Putative uncharacterized protein - Mus musculus (Mouse).
Q3U106_MOUSE Putative uncharacterized protein - Mus musculus (Mouse).
Q5H8V1_HUMAN BAFF receptor - Homo sapiens (Human).
Q8R4W8_MOUSE TRAF3 binding protein - Mus musculus (Mouse).
TR13C_HUMAN Tumor necrosis factor receptor superfamily member 13C - Homo sapiens (Human).
TR13C_MOUSE Tumor necrosis factor receptor superfamily member 13C - Mus musculus (Mouse).
Scan History
SPTR57_40f 2  300  NSINGLE    
Initial Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
PTQCNQTECFDP TR13C_MOUSE 19 19 -
PTPCVPAECFDL TR13C_HUMAN 16 16 -
GASCLSSQCFDP Q3BK46_CHICK 16 16 -

Motif 2 width=10
Element Seqn Id St Int Rpt
LLVGAPALLG TR13C_MOUSE 72 41 -
LLFGAPALLG TR13C_HUMAN 77 49 -
LIFGVPVLVG Q3BK46_CHICK 69 41 -

Motif 3 width=20
Element Seqn Id St Int Rpt
HSVPVPATELGSTELVTTKT TR13C_MOUSE 151 69 -
HSVPVPATELGSTELVTTKT TR13C_HUMAN 159 72 -
HSFPLPATELGATALVTTKT Q3BK46_CHICK 184 105 -
Final Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
PTQCNQTECFDP Q3SXS6_MOUSE 19 19 -
PTQCNQTECFDP TR13C_MOUSE 19 19 -
PTQCNQTECFDP Q8R4W8_MOUSE 19 19 -
PTQCNQTECFDP Q3U106_MOUSE 19 19 -
PTQCNQTECFDP Q3SXS7_MOUSE 19 19 -
PTPCVPAECFDL Q5H8V1_HUMAN 16 16 -
PTPCVPAECFDL TR13C_HUMAN 16 16 -
GASCLSSQCFDP Q3BK46_CHICK 16 16 -

Motif 2 width=10
Element Seqn Id St Int Rpt
LLVGAPALLG Q3SXS6_MOUSE 72 41 -
LLVGAPALLG TR13C_MOUSE 72 41 -
LLVGAPALLG Q8R4W8_MOUSE 72 41 -
LLVGAPALLG Q3U106_MOUSE 108 77 -
LLVGAPALLG Q3SXS7_MOUSE 72 41 -
LLFGAPALLG Q5H8V1_HUMAN 77 49 -
LLFGAPALLG TR13C_HUMAN 77 49 -
LIFGVPVLVG Q3BK46_CHICK 69 41 -

Motif 3 width=20
Element Seqn Id St Int Rpt
HSVPVPATELGSTELVTTKT Q3SXS6_MOUSE 151 69 -
HSVPVPATELGSTELVTTKT TR13C_MOUSE 151 69 -
HSVPVPATELGSTELVTTKT Q8R4W8_MOUSE 151 69 -
HSVPVPATELGSTELVTTKT Q3U106_MOUSE 176 58 -
HSVPVPATELGSTELVTTKT Q3SXS7_MOUSE 140 58 -
HSVPVPATELGSTELVTTKT Q5H8V1_HUMAN 159 72 -
HSVPVPATELGSTELVTTKT TR13C_HUMAN 159 72 -
HSFPLPATELGATALVTTKT Q3BK46_CHICK 184 105 -