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(-) Description

Title :  MOLECULAR FEATURES OF THE COLLAGEN V HEPARIN BINDING SITE THEORETICAL MODEL
 
Authors :  F. Delacoux, A. Fichard, C. Geourjon, R. Garrone, F. Ruggiero
Date :  03 Apr 98  (Deposition) - 21 Oct 98  (Release) - 18 Nov 98  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B,C
Keywords :  Homotrimer Collagen [Alpha (1)V]3, Heparin Binding Site Extracellular Matrix, Connective Tissue, Homotrimer Collagen [Alpha (1)V]3, Heparin Binding Site (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Delacoux, A. Fichard, C. Geourjon, R. Garrone, F. Ruggiero
Molecular Features Of The Collagen V Heparin Binding Site.
J. Biol. Chem. V. 273 15069 1998
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HOMOTRIMER COLLAGEN [ALPHA 1(V)]3
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPT7-7
    FragmentHEPARIN BINDING DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1A89)

(-) Sites  (0, 0)

(no "Site" information available for 1A89)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1A89)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1A89)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 3)

Theoretical Model (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_064702P908LCO5A1_HUMANPolymorphism772211736A
B
C
P5
26
47
L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1A89)

(-) Exons   (2, 6)

Theoretical Model (2, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003718171aENSE00001191284chr9:137533620-137534142523CO5A1_HUMAN1-37370--
1.3ENST000003718173ENSE00001671369chr9:137582758-137582925168CO5A1_HUMAN37-93570--
1.5ENST000003718175ENSE00001595490chr9:137591755-137591968214CO5A1_HUMAN93-164720--
1.6ENST000003718176ENSE00001608803chr9:137593017-137593179163CO5A1_HUMAN164-218550--
1.8ENST000003718178ENSE00001626599chr9:137619112-137619243132CO5A1_HUMAN219-262440--
1.9ENST000003718179ENSE00001691616chr9:137620516-137620653138CO5A1_HUMAN263-308460--
1.10ENST0000037181710ENSE00001730929chr9:137622082-137622321240CO5A1_HUMAN309-388800--
1.11aENST0000037181711aENSE00001668386chr9:137623342-137623509168CO5A1_HUMAN389-444560--
1.12aENST0000037181712aENSE00001709465chr9:137623917-13762397357CO5A1_HUMAN445-463190--
1.13ENST0000037181713ENSE00001610762chr9:137630320-13763036142CO5A1_HUMAN464-477140--
1.14ENST0000037181714ENSE00001621867chr9:137630592-13763065463CO5A1_HUMAN478-498210--
1.15ENST0000037181715ENSE00001801127chr9:137642388-13764246275CO5A1_HUMAN499-523250--
1.16ENST0000037181716ENSE00001725424chr9:137642636-13764272893CO5A1_HUMAN524-554310--
1.17ENST0000037181717ENSE00001677197chr9:137644435-13764449157CO5A1_HUMAN555-573190--
1.18ENST0000037181718ENSE00001683765chr9:137645696-13764574954CO5A1_HUMAN574-591180--
1.19ENST0000037181719ENSE00001656953chr9:137646119-13764617254CO5A1_HUMAN592-609180--
1.20ENST0000037181720ENSE00001755928chr9:137648611-13764866454CO5A1_HUMAN610-627180--
1.21ENST0000037181721ENSE00001709109chr9:137650089-13765014254CO5A1_HUMAN628-645180--
1.22ENST0000037181722ENSE00001655385chr9:137653771-13765382454CO5A1_HUMAN646-663180--
1.23ENST0000037181723ENSE00001606466chr9:137655539-13765558345CO5A1_HUMAN664-678150--
1.24ENST0000037181724ENSE00001782057chr9:137657527-13765758054CO5A1_HUMAN679-696180--
1.25ENST0000037181725ENSE00001707312chr9:137658300-13765834445CO5A1_HUMAN697-711150--
1.26ENST0000037181726ENSE00001630979chr9:137658846-13765889954CO5A1_HUMAN712-729180--
1.27ENST0000037181727ENSE00001692959chr9:137659156-13765920045CO5A1_HUMAN730-744150--
1.28ENST0000037181728ENSE00001679174chr9:137660256-13766030954CO5A1_HUMAN745-762180--
1.29ENST0000037181729ENSE00001806089chr9:137664636-13766468045CO5A1_HUMAN763-777150--
1.30ENST0000037181730ENSE00001688188chr9:137666705-13766675854CO5A1_HUMAN778-795180--
1.31ENST0000037181731ENSE00001687147chr9:137671948-13767199245CO5A1_HUMAN796-810150--
1.32ENST0000037181732ENSE00001676930chr9:137674513-13767456654CO5A1_HUMAN811-828180--
1.33ENST0000037181733ENSE00001722961chr9:137676835-137676942108CO5A1_HUMAN829-864360--
1.34ENST0000037181734ENSE00001764753chr9:137677841-13767789454CO5A1_HUMAN865-882180--
1.35ENST0000037181735ENSE00001604675chr9:137681001-13768105454CO5A1_HUMAN883-900180--
1.36ENST0000037181736ENSE00001610158chr9:137686928-13768697245CO5A1_HUMAN901-915153A:1-12
B:22-33
C:43-54
12
12
12
1.37ENST0000037181737ENSE00001776421chr9:137687108-13768716154CO5A1_HUMAN916-933183A:13-21
B:34-42
C:55-63
9
9
9
1.38ENST0000037181738ENSE00001643672chr9:137688220-13768826445CO5A1_HUMAN934-948150--
1.39ENST0000037181739ENSE00001658157chr9:137688694-13768874754CO5A1_HUMAN949-966180--
1.40ENST0000037181740ENSE00001604658chr9:137690254-13769030754CO5A1_HUMAN967-984180--
1.41ENST0000037181741ENSE00001705181chr9:137693800-13769385354CO5A1_HUMAN985-1002180--
1.42ENST0000037181742ENSE00001609987chr9:137694734-137694841108CO5A1_HUMAN1003-1038360--
1.43ENST0000037181743ENSE00001732370chr9:137696821-13769691090CO5A1_HUMAN1039-1068300--
1.44ENST0000037181744ENSE00001645745chr9:137697007-13769706054CO5A1_HUMAN1069-1086180--
1.45ENST0000037181745ENSE00001612894chr9:137698035-137698142108CO5A1_HUMAN1087-1122360--
1.46bENST0000037181746bENSE00001612975chr9:137701029-137701136108CO5A1_HUMAN1123-1158360--
1.47aENST0000037181747aENSE00001633601chr9:137702101-13770215454CO5A1_HUMAN1159-1176180--
1.48ENST0000037181748ENSE00001601124chr9:137703185-13770323854CO5A1_HUMAN1177-1194180--
1.49ENST0000037181749ENSE00001657240chr9:137703338-137703445108CO5A1_HUMAN1195-1230360--
1.50ENST0000037181750ENSE00001642783chr9:137704295-13770434854CO5A1_HUMAN1231-1248180--
1.51ENST0000037181751ENSE00001638324chr9:137704451-137704558108CO5A1_HUMAN1249-1284360--
1.52ENST0000037181752ENSE00001720016chr9:137705829-13770588254CO5A1_HUMAN1285-1302180--
1.53ENST0000037181753ENSE00001633287chr9:137706643-137706750108CO5A1_HUMAN1303-1338360--
1.54ENST0000037181754ENSE00001701581chr9:137707422-13770747554CO5A1_HUMAN1339-1356180--
1.55ENST0000037181755ENSE00001683541chr9:137707781-13770783454CO5A1_HUMAN1357-1374180--
1.56ENST0000037181756ENSE00001766114chr9:137708872-13770892554CO5A1_HUMAN1375-1392180--
1.57ENST0000037181757ENSE00001777093chr9:137709624-13770967754CO5A1_HUMAN1393-1410180--
1.58ENST0000037181758ENSE00001640876chr9:137710502-137710609108CO5A1_HUMAN1411-1446360--
1.59ENST0000037181759ENSE00001650767chr9:137710694-13771074754CO5A1_HUMAN1447-1464180--
1.60ENST0000037181760ENSE00001744103chr9:137710846-13771089954CO5A1_HUMAN1465-1482180--
1.61ENST0000037181761ENSE00001714785chr9:137711962-137712069108CO5A1_HUMAN1483-1518360--
1.62ENST0000037181762ENSE00001610977chr9:137713943-13771399654CO5A1_HUMAN1519-1536180--
1.63bENST0000037181763bENSE00001749345chr9:137714844-13771487936CO5A1_HUMAN1537-1548120--
1.64ENST0000037181764ENSE00001613970chr9:137715262-13771531554CO5A1_HUMAN1549-1566180--
1.65aENST0000037181765aENSE00001739898chr9:137716446-137716701256CO5A1_HUMAN1567-1652860--
1.66ENST0000037181766ENSE00001128543chr9:137717638-137717750113CO5A1_HUMAN1652-1689380--
1.67aENST0000037181767aENSE00001096530chr9:137721822-13772189069CO5A1_HUMAN1690-1712230--
1.69ENST0000037181769ENSE00002158535chr9:137726817-137727050234CO5A1_HUMAN1713-1790780--
1.70bENST0000037181770bENSE00001456153chr9:137734003-1377366862684CO5A1_HUMAN1791-1838480--

(-) Sequences/Alignments

Theoretical Model
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:21
 aligned with CO5A1_HUMAN | P20908 from UniProtKB/Swiss-Prot  Length:1838

    Alignment length:21
                                   913       923 
          CO5A1_HUMAN   904 GKPGPRGQRGPTGPRGERGPR 924
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author ..................... Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
               Transcript 1 Exon 1.36   Exon 1.37 Transcript 1
                 1a89 A   1 GKPGPRGQRGPTGPRGERGPR  21
                                    10        20 

Chain B from PDB  Type:PROTEIN  Length:21
 aligned with CO5A1_HUMAN | P20908 from UniProtKB/Swiss-Prot  Length:1838

    Alignment length:21
                                   913       923 
          CO5A1_HUMAN   904 GKPGPRGQRGPTGPRGERGPR 924
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author ..................... Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
               Transcript 1 Exon 1.36   Exon 1.37 Transcript 1
                 1a89 B  22 GKPGPRGQRGPTGPRGERGPR  42
                                    31        41 

Chain C from PDB  Type:PROTEIN  Length:21
 aligned with CO5A1_HUMAN | P20908 from UniProtKB/Swiss-Prot  Length:1838

    Alignment length:21
                                   913       923 
          CO5A1_HUMAN   904 GKPGPRGQRGPTGPRGERGPR 924
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author ..................... Sec.struct. author
                 SAPs(SNPs) ----L---------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
               Transcript 1 Exon 1.36   Exon 1.37 Transcript 1
                 1a89 C  43 GKPGPRGQRGPTGPRGERGPR  63
                                    52        62 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1A89)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1A89)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1A89)

(-) Gene Ontology  (29, 29)

Theoretical Model(hide GO term definitions)
Chain A,B,C   (CO5A1_HUMAN | P20908)
molecular function
    GO:0005201    extracellular matrix structural constituent    The action of a molecule that contributes to the structural integrity of the extracellular matrix.
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0048407    platelet-derived growth factor binding    Interacting selectively and non-covalently with platelet-derived growth factor.
    GO:0043394    proteoglycan binding    Interacting selectively and non-covalently with a proteoglycan, any glycoprotein in which the carbohydrate units are glycosaminoglycans.
biological process
    GO:0001568    blood vessel development    The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0032964    collagen biosynthetic process    The chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
    GO:0030574    collagen catabolic process    The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
    GO:0030199    collagen fibril organization    Any process that determines the size and arrangement of collagen fibrils within an extracellular matrix.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    GO:0048592    eye morphogenesis    The process in which the anatomical structures of the eye are generated and organized.
    GO:0003007    heart morphogenesis    The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0045112    integrin biosynthetic process    The chemical reactions and pathways resulting in the formation of integrins, a large family of transmembrane proteins that act as receptors for cell-adhesion molecules.
    GO:1903225    negative regulation of endodermal cell differentiation    Any process that stops, prevents or reduces the frequency, rate or extent of endodermal cell differentiation.
    GO:0051128    regulation of cellular component organization    Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
    GO:0043588    skin development    The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue.
    GO:0035989    tendon development    The process whose specific outcome is the progression of a tendon over time, from its formation to the mature structure. A tendon is a fibrous, strong, connective tissue that connects muscle to bone or integument and is capable of withstanding tension. Tendons and muscles work together to exert a pulling force.
    GO:0035313    wound healing, spreading of epidermal cells    The migration of an epidermal cell along or through a wound gap that contributes to the reestablishment of a continuous epidermis.
cellular component
    GO:0005604    basement membrane    A thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.
    GO:0005581    collagen trimer    A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures.
    GO:0005588    collagen type V trimer    A collagen heterotrimer containing type V alpha chains; [alpha1(V)]2alpha2(V) and alpha1(V)alpha2(V)alpha3(V) trimers have been observed; type V collagen triple helices associate to form fibrils.
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        CO5A1_HUMAN | P209081a9a

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