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(-)Theoretical Model
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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  THEORETICAL MODEL OF HUMAN NIDOGEN YWTD BETA-PROPELLER DOMAIN
 
Authors :  T. A. Springer
Date :  15 Sep 98  (Deposition) - 16 Dec 98  (Release) - 29 Dec 99  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Nidogen, Entactin, Laminin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. A. Springer
An Extracellular Beta-Propeller Module Predicted In Lipoprotein And Scavenger Receptors, Tyrosine Kinases, Epidermal Growth Factor Precursor, And Extracellular Matrix Components
J. Mol. Biol. V. 283 837 1998
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (NIDOGEN)
    Cellular LocationEXTRACELLULAR
    ChainsA
    FragmentYWTD DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymENTACTIN

 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 1NDX)

(-) Sites  (0, 0)

(no "Site" information available for 1NDX)

(-) SS Bonds  (2, 2)

Theoretical Model
No.Residues
1A:987 -A:1205
2A:1124 -A:1135

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Gln A:1188 -Pro A:1189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Theoretical Model (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_055764K970ENID1_HUMANPolymorphism16833060AK970E
2UniProtVAR_035835F1036SNID1_HUMANUnclassified  ---AF1036S
3CancerSNPVAR_NID1_HUMAN_CCDS1608_1_01 *F1036SNID1_HUMANDisease (Colorectal cancer)  ---AF1036S
4UniProtVAR_055765L1163VNID1_HUMANPolymorphism16833032AL1163V
   * ID not provided by source

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

(-) PROSITE Motifs  (1, 4)

Theoretical Model (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LDLRBPS51120 LDL-receptor class B (LDLRB) repeat profile.NID1_HUMAN990-1032
1033-1075
1076-1120
1121-1162
  4A:990-1032
A:1033-1075
A:1076-1120
A:1121-1162

(-) Exons   (6, 6)

Theoretical Model (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002641871bENSE00001935339chr1:236228462-236228155308NID1_HUMAN1-75750--
1.2bENST000002641872bENSE00001022663chr1:236212289-236211990300NID1_HUMAN76-1751000--
1.3ENST000002641873ENSE00001022662chr1:236208983-236208757227NID1_HUMAN176-251760--
1.4ENST000002641874ENSE00001022668chr1:236205592-236205210383NID1_HUMAN251-3791290--
1.5ENST000002641875ENSE00001022661chr1:236201553-236201404150NID1_HUMAN379-429510--
1.6ENST000002641876ENSE00001022658chr1:236195952-236195701252NID1_HUMAN429-513850--
1.7ENST000002641877ENSE00001022659chr1:236193050-236192850201NID1_HUMAN513-580680--
1.8ENST000002641878ENSE00000793467chr1:236189441-236189196246NID1_HUMAN580-662830--
1.9ENST000002641879ENSE00000793466chr1:236187513-236187370144NID1_HUMAN662-710490--
1.10ENST0000026418710ENSE00000793465chr1:236180573-236180448126NID1_HUMAN710-752430--
1.11bENST0000026418711bENSE00000793464chr1:236176860-236176711150NID1_HUMAN752-802510--
1.13ENST0000026418713ENSE00000793463chr1:236175343-236175221123NID1_HUMAN802-843420--
1.14ENST0000026418714ENSE00000793462chr1:236157172-236156945228NID1_HUMAN843-919770--
1.15ENST0000026418715ENSE00000793461chr1:236154358-236154186173NID1_HUMAN919-976581A:941-97636
1.16ENST0000026418716ENSE00000793460chr1:236148805-236148679127NID1_HUMAN977-1019431A:977-101943
1.17ENST0000026418717ENSE00000793459chr1:236145082-236144911172NID1_HUMAN1019-1076581A:1019-107658
1.18ENST0000026418718ENSE00000793458chr1:236143953-236143796158NID1_HUMAN1076-1129541A:1076-112954
1.19ENST0000026418719ENSE00000793457chr1:236143245-236143122124NID1_HUMAN1129-1170421A:1129-117042
1.20ENST0000026418720ENSE00000793456chr1:236142407-236142295113NID1_HUMAN1170-1208391A:1170-120637
1.21ENST0000026418721ENSE00001442138chr1:236141288-2361391302159NID1_HUMAN1208-1247400--

(-) 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:266
 aligned with NID1_HUMAN | P14543 from UniProtKB/Swiss-Prot  Length:1247

    Alignment length:266
                                   950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      
          NID1_HUMAN    941 PPGTHLLFAQTGKIERLPLEGNTMRKTEAKAFLHVPAKVIIGLAFDCVDKMVYWTDITEPSIGRASLHGGEPTTIIRQDLGSPEGIAVDHLGRNIFWTDSNLDRIEVAKLDGTQRRVLFETDLVNPRGIVTDSVRGNLYWTDWNRDNPKIETSYMDGTNRRILVQDDLGLPNGLTFDAFSSQLCWVDAGTNRAECLNPSQPSRRKALEGLQYPFAVTSYGKNLYFTDWKMNSVVALDLAISKETDAFQPHKQTRLYGITTALSQCP 1206
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..eeeeee............eeee.....eeeeee.....eeeeee....eeeeee.....eeeeee.....eeeeeeee...eeeeee.....eeeee....eeeee.......eeeeee.....eeeeee......eeeeee.....eeeee......eeeeee......eeeee.hhheeeeee....eeeeee.....eeeee....eeeeee....eeeeee....eeeeee.......eeeeeee..... Sec.struct. author
             SAPs(SNPs) (1) -----------------------------E-----------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------V------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------S-------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------------------LDLRB  PDB: A:990-1032 UniProt: 990-1032   LDLRB  PDB: A:1033-1075 UniProt: 1033-1075 LDLRB  PDB: A:1076-1120 UniProt: 1076-1120   LDLRB  PDB: A:1121-1162 UniProt: 1121-1162-------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.15  PDB: A:941-976           Exon 1.16  PDB: A:977-1019                 --------------------------------------------------------Exon 1.18  PDB: A:1076-1129 UniProt: 1076-1129        ----------------------------------------Exon 1.20  PDB: A:1170-1206           Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------Exon 1.17  PDB: A:1019-1076 UniProt: 1019-1076            ----------------------------------------------------Exon 1.19  PDB: A:1129-1170               ------------------------------------ Transcript 1 (2)
                1ndx A  941 PPGTHLLFAQTGKIERLPLEGNTMRKTEAKAFLHVPAKVIIGLAFDCVDKMVYWTDITEPSIGRASLHGGEPTTIIRQDLGSPEGIAVDHLGRNIFWTDSNLDRIEVAKLDGTQRRVLFETDLVNPRGIVTDSVRGNLYWTDWNRDNPKIETSYMDGTNRRILVQDDLGLPNGLHFDAFSSQLCWVDAGTNRAECLNPSQPSRRKALEGLQYPFAVTSYGKNLYFTDWKMNSVVALDLAISKETDAFQPHKQTRLYGITTALSQCP 1206
                                   950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      

   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 1NDX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Theoretical Model(hide GO term definitions)
Chain A   (NID1_HUMAN | P14543)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0005518    collagen binding    Interacting selectively and non-covalently with collagen, 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:0050840    extracellular matrix binding    Interacting selectively and non-covalently with a component of the extracellular matrix.
    GO:0043236    laminin binding    Interacting selectively and non-covalently with laminins, glycoproteins that are major constituents of the basement membrane of cells.
    GO:0043237    laminin-1 binding    Interacting selectively and non-covalently with laminin-1, a glycoprotein trimer with the subunit composition alpha1, beta1, gamma1.
    GO:0043394    proteoglycan binding    Interacting selectively and non-covalently with a proteoglycan, any glycoprotein in which the carbohydrate units are glycosaminoglycans.
biological process
    GO:0071711    basement membrane organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the basement membrane.
    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:0007160    cell-matrix adhesion    The binding of a cell to the extracellular matrix via adhesion molecules.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the 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:0032836    glomerular basement membrane development    The process whose specific outcome is the progression of the glomerular basement membrane over time, from its formation to the mature structure. The glomerular basement membrane is the basal laminal portion of the glomerulus which performs the actual filtration.
    GO:0010811    positive regulation of cell-substrate adhesion    Any process that increases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules.
cellular component
    GO:0005605    basal lamina    A thin sheet of proteoglycans and glycoproteins, especially laminin, secreted by cells as an extracellular matrix.
    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:0071944    cell periphery    The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
    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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