SPRINT Home UMBER Home Contents Standard Search Advanced Search Relation Search

==SPRINT==> PRINTS View



  selected as


PR01633

Identifier
RVDCCALPHA1  [View Relations]  [View Alignment]  
Accession
PR01633
No. of Motifs
6
Creation Date
11-DEC-2001
Title
R-type voltage-dependent calcium channel alpha-1 subunit signature
Database References
PRINTS; PR00167 CACHANNEL
Literature References
1. WILLIAMS, M.E., BRUST. P.F., FELDMAN, D.H., PATTHI, S., SIMERSON, S., 
MAROUFI, A., MCCUE, A.F., VELICELBI, G., ELLIS, S.B. AND HARPOLD, M.M.
Structure and functional expression of an omega-conotoxin sensitive human
N-type calcium channel.
SCIENCE 257 389-395 (1992).
 
2. MORI, Y., FRIEDRICH, T., KIM, MS., MIKAMI, A., NAKAI, J., RUTH, P., 
BOSSE, E., HOFMANN, F., FLOCKERZI, V., FURUICHI, T., MIKOSHIBA, K., 
IMOTO, K., TANABE, T. AND NUMA, S.
Primary structure and functional expression from complementary DNA of a 
brain calcium channel.
NATURE 350 398-402 (1991).
 
3. ASHCROFT, F.M.
Voltage-gated Ca2+ channels.
IN ION CHANNELS AND DISEASE, ACADEMIC PRESS, 2000, PP.161-183.
 
4. KOCH, W.J., ELLINOR, P.T. AND SCHWARTZ, A.
cDNA cloning of a dihydropyridine-sensitive calcium channel from rat aorta -
evidence for the existence of alternatively spliced forms.
J.BIOL.CHEM. 265(29) 17786-17791 (1990).
 
5. RANDALL, A.D. AND TSIEN, R.W.
Contrasting biophysical and pharmacological properties of T-type and R-type
calcium channels.
NEUROPHARMACOLOGY 36(7) 879-893 (1997).
 
6. FOEHRING, R.C., MERMELSTEIN, P.G., SONG, W., ULRICH, S. AND SURMEIER, D.J.
Unique properties of R-type calcium currents in neocortical and neostriatal
neurons.
J.NEUROPHYSIOL. 84(5) 2225-2236 (2000).
 
7. GASPARINI, S., KASYANOV, A.M., PIETROBON, D., VORONIN, L.L. AND
CHERUBINI, E.
Presynaptic R-type calcium channels contribute to fast excitatory synaptic
transmission in the rat hippocampus.
J.NEUROSCI. 21(22) 8715-8721 (2001).

Documentation
Calcium channel proteins are involved in the control of neurotransmitter
release from neurons [1], and play an important role in the regulation of a
variety of cellular functions, including membrane excitability, muscle
contraction and synaptic transmission [2]. Voltage-gated calcium channels
are classified as T, L, N, P, Q and R, and are distinguished by their
sensitivity to pharmacological blocks, single-channel conductance kinetics,
and voltage-dependence. On the basis of their voltage activation
properties, the voltage-gated calcium classes can be further divided into
two broad groups: the low (T-type) and high (L, N, P, Q and R-type)
threshold-activated channels [3].
 
Generally, the channel proteins are composed of 4 tightly-coupled subunits
(alpha-1, alpha-2, beta and gamma), the alpha-1 subunit from each creating
the pore for the import of extracellular calcium ions. The alpha-1 subunit
shares sequence characteristics with all voltage-dependent cation channels,
and exploits the same 6-helix bundle structural motif - in both sodium and
calcium channels, this motif is repeated 4 times within the sequence to give
a 24-helix bundle. Within each of these repeats, 5 of the transmembrane (TM)
segments (S1, S2, S3, S5, S6) are hydrophobic and one is positively charged
(S4) - the latter is characterised by charged amino acids at very third
position, and probably represents the voltage-sensor.
 
Several genes encoding alpha-1 subunits have been identified, each forming
a distinct electrophysiological channel [4]. R-type calcium channels are
composed of alpha-1E subunits and are found in a variety of neuronal
populations, such as cerebellar granule neurons and dendrites of hippocampal
pyrimidal neurons [5]. They are believed to play an important role in the
body's natural communication network, where they contribute to the 
regulation of brain function by synaptic integration [6]. Their hypolarised
inactivation range and rapid kinetics of inactivation make R-type channels
more suited to providing a transient surge of Ca2+ influx [6,7].
 
RVDCCALPHA1 is a 6-element fingerprint that provides a signature for the
R-type voltage-dependent calcium channel alpha-1 subunit. The fingerprint
was derived from an initial alignment of 5 sequences: the motifs were drawn
from conserved regions spanning the N-terminal half of the alignment: motifs
1 and 2 lie in the extracellular region between TM domains 5 and 6 of repeat
I; motif 3 resides in the cytoplasmic region between TM domain 6 of repeat I
and TM domain 1 of repeat II; and motifs 4-6 span the cytoplasmic region 
between TM domain 6 of repeat II and TM domain 1 of repeat III. A single
iteration on SPTR40_18f was required to reach convergence, no further 
sequences being identified beyond the starting set.
Summary Information
5 codes involving  6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
6555555
5000000
4000000
3000000
2000000
123456
True Positives
CB21_RABIT    CCAE_DISOM    CCT1_RAT      Q15878        
Q61290
Sequence Titles
CB21_RABIT  BRAIN CALCIUM CHANNEL BII-1 PROTEIN - ORYCTOLAGUS CUNICULUS (RABBIT). 
CCAE_DISOM Probable voltage-dependent R-type calcium channel alpha-1E subunit (DOE-1) - Discopyge ommata (Electric ray).
CCT1_RAT NICKEL-SENSITIVE T-TYPE CALCIUM CHANNEL ALPHA-1 SUBUNIT (RBE-II) - RATTUS NORVEGICUS (RAT).
Q15878 VOLTAGE-OPERATED CALCIUM CHANNEL, ALPHA-1 SUBUNIT - HOMO SAPIENS (HUMAN).
Q61290 DIHYDROPYRIDINE-SENSITIVE L-TYPE, CALCIUM CHANNEL ALPHA-1D SUBUNIT (ALPHA-1E) - MUS MUSCULUS (MOUSE).
Scan History
SPTR40_18f 1  170  NSINGLE    
Initial Motifs
Motif 1  width=15
Element Seqn Id St Int Rpt
ILEGFDPPHPCGVQG CCT1_RAT 209 209 -
ILEGFDPPHPCGVQG Q15878 258 258 -
ILEGFDPPHPCGVQG Q61290 259 259 -
VLEGFDPPHPCGVQG CB21_RABIT 258 258 -
AAEELDLQFPCGTQE CCAE_DISOM 266 266 -

Motif 2 width=12
Element Seqn Id St Int Rpt
CPAGYECKDWIG CCT1_RAT 224 0 -
CPAGYECKDWIG Q15878 273 0 -
CPAGYECKDWIG Q61290 274 0 -
CPAGYECKDWIG CB21_RABIT 273 0 -
CPNGTVCSYWIG CCAE_DISOM 285 4 -

Motif 3 width=13
Element Seqn Id St Int Rpt
RHKERLLRISIRH CCT1_RAT 410 174 -
RHKERLLRISIRH Q15878 459 174 -
RHKERLLRISIRH Q61290 460 174 -
RHKERLLRISVRH CB21_RABIT 459 174 -
RRKERMLRISIRH CCAE_DISOM 473 176 -

Motif 4 width=14
Element Seqn Id St Int Rpt
SCHGNCDPTQQETG CCT1_RAT 838 415 -
PCHGNCDPTQQEAG Q15878 886 414 -
SCHGNCDPIQQEAG Q61290 888 415 -
PCHGNCEPALQETA CB21_RABIT 878 406 -
GEQGRALGRSVEAG CCAE_DISOM 866 380 -

Motif 5 width=11
Element Seqn Id St Int Rpt
GKESASASRSR CCT1_RAT 881 29 -
GKESSSASRSR Q15878 929 29 -
GKDSASASRSR Q61290 931 29 -
AKESSSASRSR CB21_RABIT 921 29 -
LEESAETSLSR CCAE_DISOM 905 25 -

Motif 6 width=20
Element Seqn Id St Int Rpt
TTESTSVTVAIPDVDPLVDS CCT1_RAT 1016 124 -
TTESTSVTVAIPDVDPLVDS Q15878 1063 123 -
TTESTSVTVAIPDVDPLVDS Q61290 1066 124 -
TTESTDVTVAIPDAEPLVDS CB21_RABIT 1055 123 -
TQEQTEIDVDCENTETPMDS CCAE_DISOM 1036 120 -
Final Motifs
Motif 1  width=15
Element Seqn Id St Int Rpt
ILEGFDPPHPCGVQG CCT1_RAT 209 209 -
ILEGFDPPHPCGVQG Q15878 258 258 -
ILEGFDPPHPCGVQG Q61290 259 259 -
VLEGFDPPHPCGVQG CB21_RABIT 258 258 -
AAEELDLQFPCGTQE CCAE_DISOM 266 266 -

Motif 2 width=12
Element Seqn Id St Int Rpt
CPAGYECKDWIG CCT1_RAT 224 0 -
CPAGYECKDWIG Q15878 273 0 -
CPAGYECKDWIG Q61290 274 0 -
CPAGYECKDWIG CB21_RABIT 273 0 -
CPNGTVCSYWIG CCAE_DISOM 285 4 -

Motif 3 width=13
Element Seqn Id St Int Rpt
RHKERLLRISIRH CCT1_RAT 410 174 -
RHKERLLRISIRH Q15878 459 174 -
RHKERLLRISIRH Q61290 460 174 -
RHKERLLRISVRH CB21_RABIT 459 174 -
RRKERMLRISIRH CCAE_DISOM 473 176 -

Motif 4 width=14
Element Seqn Id St Int Rpt
SCHGNCDPTQQETG CCT1_RAT 838 415 -
PCHGNCDPTQQEAG Q15878 886 414 -
SCHGNCDPIQQEAG Q61290 888 415 -
PCHGNCEPALQETA CB21_RABIT 878 406 -
GEQGRALGRSVEAG CCAE_DISOM 866 380 -

Motif 5 width=11
Element Seqn Id St Int Rpt
GKESASASRSR CCT1_RAT 881 29 -
GKESSSASRSR Q15878 929 29 -
GKDSASASRSR Q61290 931 29 -
AKESSSASRSR CB21_RABIT 921 29 -
LEESAETSLSR CCAE_DISOM 905 25 -

Motif 6 width=20
Element Seqn Id St Int Rpt
TTESTSVTVAIPDVDPLVDS CCT1_RAT 1016 124 -
TTESTSVTVAIPDVDPLVDS Q15878 1063 123 -
TTESTSVTVAIPDVDPLVDS Q61290 1066 124 -
TTESTDVTVAIPDAEPLVDS CB21_RABIT 1055 123 -
TQEQTEIDVDCENTETPMDS CCAE_DISOM 1036 120 -