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(-) Description

Title :  MURINE ENDOSTATIN, CRYSTAL FORM III
 
Authors :  E. Hohenester, T. Sasaki, R. Timpl
Date :  21 Jan 00  (Deposition) - 21 Jan 01  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Angiogenesis Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Hohenester, T. Sasaki, K. Mann, R. Timpl
Variable Zinc Coordination In Endostatin
J. Mol. Biol. V. 297 1 2000
PubMed-ID: 10704302  |  Reference-DOI: 10.1006/JMBI.2000.3553
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COLLAGEN ALPHA1(XVIII) CHAIN
    ChainsA
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System CellEMBRYONIC KIDNEY CELL
    Expression System Cell LineEBNA-293
    Expression System Taxid9606
    Expression System VectorPCEP-PU
    FragmentENDOSTATIN DOMAIN
    MutationYES
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:132 , HIS A:134 , HIS A:142 , ASP A:207BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREALA A:128 , HIS A:297 , HOH A:2046 , HOH A:2047BINDING SITE FOR RESIDUE ZN A 402

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:164 -A:304
2A:266 -A:296

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DY1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DY1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DY1)

(-) Exons   (0, 0)

(no "Exon" information available for 1DY1)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:183
 aligned with COIA1_MOUSE | P39061 from UniProtKB/Swiss-Prot  Length:1774

    Alignment length:183
                                  1596      1606      1616      1626      1636      1646      1656      1666      1676      1686      1696      1706      1716      1726      1736      1746      1756      1766   
         COIA1_MOUSE   1587 LSLAHTHQDFQPVLHLVALNTPLSGGMRGIRGADFQCFQQARAVGLSGTFRAFLSSRLQDLYSIVRRADRGSVPIVNLKDEVLSPSWDSLFSGSQGQLQPGARIFSFDGRDVLRHPAWPQKSVWHGSDPSGRRLMESYCETWRTETTGATGQASSLLSGRLLEQKAASCHNSYIVLCIENSFM 1769
               SCOP domains d1dy1a_ A: Endostatin                                                                                                                                                                   SCOP domains
               CATH domains 1dy1A00 A:128-310 Mannose-Binding Protein A, subunit A                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.........hhhhhhhhhhhhhhhhh.....eee.......hhhhhhhhhhh....ee.....eee..hhhhhh.............................eee.............hhhhhh......eeeeee.hhh.....eeee.......eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1dy1 A  128 APLAHTHQDFQPVLHLVALNTPLSGGMRGIRGADFQCFQQARAVGLSGTFRAFLSSRLQDLYSIVRRADRGSVPIVNLKDEVLSPSWDSLFSGSQGQLQPGARIFSFDGRDVLRHPAWPQKSVWHGSDPSGRRLMESYCETWRTETTGATGQASSLLSGRLLEQKAASCHNSYIVLCIENSFM  310
                                   137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307   

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DY1)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (COIA1_MOUSE | P39061)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    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:0001886    endothelial cell morphogenesis    The change in form (cell shape and size) that occurs during the differentiation of an endothelial cell.
    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:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:2000353    positive regulation of endothelial cell apoptotic process    Any process that activates or increases the frequency, rate or extent of endothelial cell apoptotic process.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0051599    response to hydrostatic pressure    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrostatic pressure stimulus. Hydrostatic pressure is the force acting on an object in a system where the fluid is at rest (as opposed to moving). The weight of the fluid above the object creates pressure on it.
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: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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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)

UniProtKB/Swiss-Prot
        COIA1_MOUSE | P390611dy0 1koe

(-) Related Entries Specified in the PDB File

1dy0 MURINE ENDOSTATIN, CRYSTAL FORM II MOLECULE: COLLAGEN ALPHA1(XVIII) CHAIN
1dy2 MURINE COLLAGEN ALPHA1(XV), ENDOSTATIN DOMAIN MURINE ENDOSTATIN, CRYSTAL FORM III, COLLAGEN ALPHA1(XVIII) CHAIN
1koe ENDOSTATIN, C-TERMINAL 184 RESIDUES OF ALPHA1 CHAIN OF COLLAGEN XVIII