LIG_RGD
ELM server details
ELM
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Functional site class:
Integrin binding sites
Functional site description:
Short peptide ligand motifs which interact directly with extracellular domains of integrins
ELM(s): LIG_IBS_1, LIG_RGD
LIG_RGD description: This motif can be found in proteins of the extracellular matrix and it is recognized by different members of the integrin family. The structure of the tenth type III module of fibronectin has shown that the RGD motif lies on a flexible loop.
Pattern: RGD
Present in taxon(s): Metazoa  
Not represented in taxon(s):

o See instances for LIG_RGD


o Abstract

Integrins are major metazoan cell surface receptors that interact with extracellular matrix proteins. They are heterodimers of alpha and beta subunits that contain a large extracellular domain responsible for ligand binding, a single transmembrane domain and a cytoplasmic domain of 20-70 amino acid residues. Integrins play central roles in cell adhesion, cell migration and control of cell differentiation, proliferation and programmed cell death. A hallmark of the integrins is the ability of individual family members to recognize multiple ligands. Most integrins recognize relatively short peptide motifs such as RGD, LDV or DLXXL and, in general, a key constituent residue is an acidic amino acid. Some collagens have another - different - integrin binding motif. The ligand specificities rely on both subunits of a given alpha-beta heterodimer. Proteins that contain RGD attachment sites together with the integrins that serve as receptors for them, constitute a major recognition system for cell adhesion. RGD was originally identified as the sequence in fibronectin that engages the fibronectin receptor, integrin alpha 5 beta 1. RGD sequences have also been found to be responsible for the cell adhesive properties of a number of other proteins, including fibrinogen, von Willebrand factor and victronectin. Many snake venoms are rich in RGD peptides – a testament to the importance of the integrin system. While their motives may be more benign, the pharmaceutical industry also finds the integrin-RGD system to be of considerable interest. Antagonists could be effective for therapeutic intervention in e.g. cancer, thrombosis and numerous inflammatory conditions.

o Selected references

Assa-Munt N, Jia X, Laakkonen P, Ruoslahti E
Solution structures and integrin binding activities of an RGD peptide with two isomers.
Biochemistry 2001 Feb 27;40(8) : 2373-8.
PMID: 11327857

Hynes RO
Integrins: bidirectional, allosteric signaling machines.
Cell 2002 Sep 20;110(6) : 673-87.
PMID: 12297042

Main AL, Harvey TS, Baron M, Boyd J, Campbell ID
The three-dimensional structure of the tenth type III module of fibronectin: an insight into RGD-mediated interactions.
Cell 1992 Nov 13;71(4) : 671-8.
PMID: 1423622

Plow EF, Haas TA, Zhang L, Loftus J, Smith JW
Ligand binding to integrins.
J Biol Chem 2000 Jul 21;275(29) : 21785-8.
PMID: 10801897

Xiong JP, Stehle T, Diefenbach B, Zhang R, Dunker R, Scott DL, Joachimiak A, Goodman SL, Arnaout MA
Crystal structure of the extracellular segment of integrin alpha Vbeta3.
Science 2001 Oct 12;294(5541) : 339-45.
PMID: 11546839

Xiong JP, Stehle T, Zhang R, Joachimiak A, Frech M, Goodman SL, Arnaout MA
Crystal structure of the extracellular segment of integrin alpha Vbeta3 in complex with an Arg-Gly-Asp ligand.
Science 2002 Apr 5;296(5565) : 151-5.
PMID: 11884718

o This ELM has been assigned the following Gene Ontology (GO) terms for biological process, cellular component and molecular function.

Biological Process
  cell-adhesion
Cellular Component
  extracellular
  integrin
Molecular Function
  integrin binding
  cell adhesion molecule

 

o Instances for LIG_RGD

SequencePositionSubsequence
(Click for evidence information)
PDBGene NameProtein DescriptionOrganism
SIAL_HUMAN 286-288 ENGEPRGDNYRAYE - Name=IBSP; Synonyms=BNSP; Bone sialoprotein 2 precursor (Bone sialoprotein II) (BSP II) (Cell- binding sialoprotein) (Integrin-binding sialoprotein). Homo sapiens (Human).
FINC_HUMAN 1524-1526 YAVTGRGDSPASSK - Name=FN1; Synonyms=FN; Fibronectin precursor (FN) (Cold-insoluble globulin) (CIG) [Contains: Ugl-Y1; Ugl-Y2; Ugl-Y3]. Homo sapiens (Human).
FINC_MOUSE 1614-1616 YAVTGRGDSPASSK - Name=Fn1; Fibronectin precursor (FN). Mus musculus (Mouse).
FINC_MOUSE 2181-2183 IGHVPRGDVDYHLY - Name=Fn1; Fibronectin precursor (FN). Mus musculus (Mouse).
EDIL3_HUMAN 96-98 ISEAYRGDTFIGYV - Name=EDIL3; Synonyms=DEL1; EGF-like repeat and discoidin I-like domain-containing protein 3 precursor (EGF-like repeats and discoidin I-like domains protein 3) (Developmentally-regulated endothelial cell locus 1 protein) (Integrin-binding protein DEL1). Homo sapiens (Human).
DISB_TRIGA 51-53 ICRRARGDDLDDYC - - Disintegrin trigramin-beta-2 (Platelet aggregation activation inhibitor) [Contains: Disintegrin trigramin-beta-1]. Trimeresurus gramineus (Indian green tree viper) (Green habu snake).
DIS1B_DICDI 79-81 VALQGRGDHDQWVT - Name=dscB-1; Synonyms=dscC-1; ORFNames=DDB_0215401; and Name=dscB-2; Synonyms=dscC-2; ORFNames=DDB_0217356; Discoidin-1 subunit B/C (Discoidin I chain C/D). Dictyostelium discoideum (Slime mold).
OSTP_HUMAN 159-161 DTYDGRGDSVVYGL - Name=SPP1; Synonyms=BNSP, OPN; ORFNames=PSEC0156; Osteopontin precursor (Bone sialoprotein 1) (Secreted phosphoprotein 1) (SPP-1) (Urinary stone protein) (Nephropontin) (Uropontin). Homo sapiens (Human).
OSTP_RAT 144-146 DVPDGRGDSLAYGL - Name=Spp1; Synonyms=2b7, Spp-1; Osteopontin precursor (Bone sialoprotein 1) (Secreted phosphoprotein 1) (SPP-1). Rattus norvegicus (Rat).
OSTP_BOVIN 152-154 SANDGRGDSVAYGL - Name=SPP1; Synonyms=OPN; Osteopontin precursor (Bone sialoprotein 1) (Secreted phosphoprotein 1) (SPP-1). Bos taurus (Bovine).
VWF_HUMAN 698-700 LYMDERGDCVPKAQ - Name=VWF; Synonyms=F8VWF; von Willebrand factor precursor (vWF) [Contains: von Willebrand antigen 2 (von Willebrand antigen II)]. Homo sapiens (Human).
VWF_HUMAN 2507-2509 VTGSPRGDSQSSWK - Name=VWF; Synonyms=F8VWF; von Willebrand factor precursor (vWF) [Contains: von Willebrand antigen 2 (von Willebrand antigen II)]. Homo sapiens (Human).
VTNC_HUMAN 64-66 KPQVTRGDVFTMPE - Name=VTN; Vitronectin precursor (Serum-spreading factor) (S-protein) (V75) [Contains: Vitronectin V65 subunit; Vitronectin V10 subunit; Somatomedin-B]. Homo sapiens (Human).
VTNC_MOUSE 64-66 KPQVTRGDVFTMPE - Name=Vtn; Vitronectin precursor (Serum-spreading factor) (S-protein). Mus musculus (Mouse).
DISG_TRIAB 51-53 ICRRARGDDLDDYC - - Disintegrin albolabrin (Platelet aggregation activation inhibitor). Trimeresurus albolabris (White-lipped pit viper).
DIS1_TRIEL 51-53 ICRRARGDNPDDRC - - Zinc metalloproteinase elegantin-1 precursor (EC 3.4.24.-) [Contains: Disintegrin elegantin-1a; Disintegrin elegantin-1b; Disintegrin elegantin-1c]. Trimeresurus elegans (Sakishima habu) (Protobothrops elegans).
SIAL_RAT 289-291 NNGEPRGDTYRAYE - Name=Ibsp; Bone sialoprotein 2 precursor (Bone sialoprotein II) (BSP II) (Cell- binding sialoprotein) (Integrin-binding sialoprotein). Rattus norvegicus (Rat).