SPRINT Home UMBER Home Contents Standard Search Advanced Search Relation Search

==SPRINT==> PRINTS View



  selected as


PR01474

Identifier
VCAM1  [View Relations]  [View Alignment]  
Accession
PR01474
No. of Motifs
6
Creation Date
15-FEB-2001
Title
Vascular cell adhesion molecule-1 (VCAM-1) signature
Database References
PRINTS; PR01472 ICAMVCAM1
PDB; 1VCA
SCOP; 1VCA
CATH; 1VCA
Literature References
1. GAHMBERG, C,G., TOLVANEN, M. AND  KOTOVUORI, P.
Leukocyte adhesion. Structure and function of human leukocyte
beta2-integrins and their cellular ligands.
EUR.J.BIOCHEMISTRY 245 215-232 (1997).
 
2. LEE, Y. W., KUHN, H., HENNIG, B., NEISH, A.S. AND TOBOREK, M.
IL-4 induced oxidative stress upregulates VCAM-1 gene expression in human
endothelial cells.
J.MOL.CELL.CARDIO. 33 83-94 (2001).
 
3. JONES, E.Y., HARLOS, K., BOTTOMLEY, M.J., ROBINSON, R.C., DRISCOLL, P.C.,
EDWARDS, R.M., CLEMENTS, J.M., DUDGEON, T.J. AND STUART, D.I.
Crystal structure of an integrin-binding fragment of vascular cell adhesion
molecule-1 at 1.8 A resolution.
NATURE 373 539-544 (1995). 

Documentation
Vascular cell adhesion molecule-1 (VCAM-1) is part of the immunoglobulin
superfamily. They are important in inflammation, immune responses and in
intracellular signalling events [1]. 
 
VCAM-1 was first described as a cytokine-inducible endothelial adhesion
molecule. It can bind to leucocyte integrin VL-4 (very late antigen-4) to 
recruit leucocytes to sites of inflammation [2]. The predominant form of
VCAM-1 in vivo has an N-terminal extracellular region comprising seven
Ig-like domains [3]. A conserved integrin-binding motif has been identified 
in domains 1 and 4, variants of which are present in the N-terminal domain
of all members of the integrin-binding subgroup of the immunoglobulin 
superfamily [3]. The structure of a VLA-4-binding fragment comprising the
first two domains of VCAM-1 has been determined to 1.8A resolution [3]. The
integrin-binding motif is exposed and forms the N-terminal region of the
loop between beta-strands C and D of domain 1 [3]. VCAM-1 domains 1 and 2
are structurally similar to ICAM-1 and ICAM-2 [2]. 
 
VCAM1 is 6-element fingerprint that a provides a signature for the VCAM-1
cell adhesion molecules. The fingerprint was derived from an initial
alignement of 3 sequences: the motifs were drawn from conserved regions 
towards the N-terminal portion of the alignment - motifs 1 and 2 lie within
the N-terminus of domain 1; and the remaining motifs lie in the N-terminal
region of domain 3. Two iterations on SPTR39_14f were required to reach
convergence, at which point a true set comprising 7 sequences was identified.
Summary Information
7 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
6777777
5000000
4000000
3000000
2000000
123456
True Positives
Q28260        Q28939        Q29123        Q63669        
VCA1_HUMAN VCA1_MOUSE VCA1_RAT
Sequence Titles
Q28260      VASCULAR CELL ADHESION MOLECULE-1 - Canis familiaris (Dog). 
Q28939 VASCULAR CELL ADHESION MOLECULE PRECURSOR - Sus scrofa (Pig).
Q29123 VASCULAR CELL ADHESION MOLECULE - Sus scrofa (Pig).
Q63669 VASCULAR CELL ADHESION MOLECULE 1 PRECURSOR - Rattus norvegicus (Rat).
VCA1_HUMAN VASCULAR CELL ADHESION PROTEIN 1 PRECURSOR (V-CAM 1) (CD106 ANTIGEN) (INCAM-100) - Homo sapiens (Human).
VCA1_MOUSE VASCULAR CELL ADHESION PROTEIN 1 PRECURSOR (V-CAM 1) - Mus musculus (Mouse).
VCA1_RAT VASCULAR CELL ADHESION PROTEIN 1 PRECURSOR (V-CAM 1) - Rattus norvegicus (Rat).
Scan History
SPTR39_14f 2  50   NSINGLE    
Initial Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
PVSFENEHSYLCTATC VCA1_RAT 84 84 -
PVSFGNEHSYLCTATC VCA1_HUMAN 84 84 -
PVSFENEHSYLCTVSC Q28939 85 85 -

Motif 2 width=13
Element Seqn Id St Int Rpt
LQVYTSPKNTEIS VCA1_RAT 217 117 -
LQVYISPKNTVIS VCA1_HUMAN 217 117 -
MQVYISPKDPVIS Q28939 215 114 -

Motif 3 width=13
Element Seqn Id St Int Rpt
EGAAVTMTCASEG VCA1_RAT 238 8 -
EGGSVTMTCSSEG VCA1_HUMAN 238 8 -
EGDSMMMTCTSEG Q28939 236 8 -

Motif 4 width=14
Element Seqn Id St Int Rpt
WSKKLDNGVLQLLS VCA1_RAT 258 7 -
WSKKLDNGNLQHLS VCA1_HUMAN 258 7 -
WSKKLDNGDQQLLS Q28939 256 7 -

Motif 5 width=11
Element Seqn Id St Int Rpt
SGNATLTLIAM VCA1_RAT 271 -1 -
SGNATLTLIAM VCA1_HUMAN 271 -1 -
SGNATLTLIAM Q28939 269 -1 -

Motif 6 width=14
Element Seqn Id St Int Rpt
RMEDSGIYVCEGVN VCA1_RAT 282 0 -
RMEDSGIYVCEGVN VCA1_HUMAN 282 0 -
RMEDSGIYVCEGVN Q28939 280 0 -
Final Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
PVSFENEHSYLCTATC Q63669 84 84 -
PVSFENEHSYLCTATC VCA1_RAT 84 84 -
PVSFGNEHSYLCTATC VCA1_HUMAN 84 84 -
PVSFNNEHAYLCTATC Q28260 84 84 -
PVSFENEHSYLCTVSC Q29123 85 85 -
PVSFENEHSYLCTATC VCA1_MOUSE 84 84 -
PVSFENEHSYLCTVSC Q28939 85 85 -

Motif 2 width=13
Element Seqn Id St Int Rpt
LQVYTSPKNTEIS Q63669 217 117 -
LQVYTSPKNTEIS VCA1_RAT 217 117 -
LQVYISPKNTVIS VCA1_HUMAN 217 117 -
LQVYISPRNTFIS Q28260 217 117 -
MQVYISPKDPVIS Q29123 215 114 -
LQVYISPRNTTIS VCA1_MOUSE 217 117 -
MQVYISPKDPVIS Q28939 215 114 -

Motif 3 width=13
Element Seqn Id St Int Rpt
EGAAVTMTCASEG Q63669 238 8 -
EGAAVTMTCASEG VCA1_RAT 238 8 -
EGGSVTMTCSSEG VCA1_HUMAN 238 8 -
EGGSVTMTCASEG Q28260 238 8 -
EGDSVMMTCTSEG Q29123 236 8 -
EGGAVTMTCSSEG VCA1_MOUSE 238 8 -
EGDSMMMTCTSEG Q28939 236 8 -

Motif 4 width=14
Element Seqn Id St Int Rpt
WSKKLDNGVLQLLS Q63669 258 7 -
WSKKLDNGVLQLLS VCA1_RAT 258 7 -
WSKKLDNGNLQHLS VCA1_HUMAN 258 7 -
WSKKLDNGNLQLLS Q28260 258 7 -
WSKKLDNGDQQLLS Q29123 256 7 -
WGRKLDNEVLQLLS VCA1_MOUSE 258 7 -
WSKKLDNGDQQLLS Q28939 256 7 -

Motif 5 width=11
Element Seqn Id St Int Rpt
SGNATLTLIAM Q63669 271 -1 -
SGNATLTLIAM VCA1_RAT 271 -1 -
SGNATLTLIAM VCA1_HUMAN 271 -1 -
SGNATLTLIAM Q28260 271 -1 -
SGNATLTLIAM Q29123 269 -1 -
SGNATLTLIAM VCA1_MOUSE 271 -1 -
SGNATLTLIAM Q28939 269 -1 -

Motif 6 width=14
Element Seqn Id St Int Rpt
RMEDSGIYVCEGVN Q63669 282 0 -
RMEDSGIYVCEGVN VCA1_RAT 282 0 -
RMEDSGIYVCEGVN VCA1_HUMAN 282 0 -
RLEDSGTYVCEGVN Q28260 282 0 -
RMEDSGIYVCEGVN Q29123 280 0 -
RMEDSGVYVCEGVN VCA1_MOUSE 282 0 -
RMEDSGIYVCEGVN Q28939 280 0 -