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(-) Description

Title :  CRYSTAL STRUCTURE OF A COLLAGEN VIII NC1 DOMAIN TRIMER
 
Authors :  M. Kvansakul, O. Bogin, E. Hohenester, A. Yayon
Date :  10 Dec 02  (Deposition) - 20 Nov 03  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Collagen, C1Q_like_domain, Extracellular Matrix, Adhesion, Connective Tissue, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Kvansakul, O. Bogin, E. Hohenester, A. Yayon
Crystal Structure Of The Collagen Alpha1(Viii) Nc1 Trimer.
Matrix Biol. V. 22 145 2003
PubMed-ID: 12782141  |  Reference-DOI: 10.1016/S0945-053X(02)00119-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COLLAGEN ALPHA 1(VIII) CHAIN
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidP89BLUESCRIPT
    Expression System Taxid562
    FragmentNONHELICAL REGION (NC1), RESIDUES 613-743
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CPS1Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:661 , ALA A:663 , SER A:702 , TYR B:661 , HIS B:665 , SER B:702 , TYR C:661 , HIS C:665 , SER C:702 , HOH C:2075 , HOH C:2111 , HOH C:2112BINDING SITE FOR RESIDUE SO4 C 900
2AC2SOFTWARETYR B:730 , GLN C:643 , CYS C:654 , TRP C:674 , TYR C:688 , PRO C:709 , GLY C:710 , GLN C:721 , HOH C:2044 , HOH C:2051 , HOH C:2099BINDING SITE FOR RESIDUE CPS C 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O91)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1O91)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O91)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1O91)

(-) Exons   (0, 0)

(no "Exon" information available for 1O91)

(-) 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:131
 aligned with CO8A1_MOUSE | Q00780 from UniProtKB/Swiss-Prot  Length:744

    Alignment length:131
                                   623       633       643       653       663       673       683       693       703       713       723       733       743 
          CO8A1_MOUSE   614 EMPAFTAELTVPFPPVGAPVKFDKLLYNGRQNYNPQTGIFTCEVPGVYYFAYHVHCKGGNVWVALFKNNEPMMYTYDEYKKGFLDQASGSAVLLLRPGDQVFLQMPSEQAAGLYAGQYVHSSFSGYLLYPM 744
               SCOP domains d1o91a_ A: Collagen NC1 trimerisation domain                                                                                        SCOP domains
               CATH domains 1o91A00 A:613-743  [code=2.60.120.40, no name defined]                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..............eeeeeehhh.............eeeeeeeeeeeeeeeeeeeeee.................eeeeeeeeeee...........hhh.eeee......eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o91 A 613 EMPAFTAELTVPFPPVGAPVKFDKLLYNGRQNYNPQTGIFTCEVPGVYYFAYHVHCKGGNVWVALFKNNEPMMYTYDEYKKGFLDQASGSAVLLLRPGDQVFLQMPSEQAAGLYAGQYVHSSFSGYLLYPM 743
                                   622       632       642       652       662       672       682       692       702       712       722       732       742 

Chain B from PDB  Type:PROTEIN  Length:131
 aligned with CO8A1_MOUSE | Q00780 from UniProtKB/Swiss-Prot  Length:744

    Alignment length:131
                                   623       633       643       653       663       673       683       693       703       713       723       733       743 
          CO8A1_MOUSE   614 EMPAFTAELTVPFPPVGAPVKFDKLLYNGRQNYNPQTGIFTCEVPGVYYFAYHVHCKGGNVWVALFKNNEPMMYTYDEYKKGFLDQASGSAVLLLRPGDQVFLQMPSEQAAGLYAGQYVHSSFSGYLLYPM 744
               SCOP domains d1o91b_ B: Collagen NC1 trimerisation domain                                                                                        SCOP domains
               CATH domains 1o91B00 B:613-743  [code=2.60.120.40, no name defined]                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..............eeeeeehhh.............eeeeeeeeeeeeeeeeeeeeee.................eeeeeeeeeee...........hhh.eeee......eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o91 B 613 EMPAFTAELTVPFPPVGAPVKFDKLLYNGRQNYNPQTGIFTCEVPGVYYFAYHVHCKGGNVWVALFKNNEPMMYTYDEYKKGFLDQASGSAVLLLRPGDQVFLQMPSEQAAGLYAGQYVHSSFSGYLLYPM 743
                                   622       632       642       652       662       672       682       692       702       712       722       732       742 

Chain C from PDB  Type:PROTEIN  Length:131
 aligned with CO8A1_MOUSE | Q00780 from UniProtKB/Swiss-Prot  Length:744

    Alignment length:131
                                   623       633       643       653       663       673       683       693       703       713       723       733       743 
          CO8A1_MOUSE   614 EMPAFTAELTVPFPPVGAPVKFDKLLYNGRQNYNPQTGIFTCEVPGVYYFAYHVHCKGGNVWVALFKNNEPMMYTYDEYKKGFLDQASGSAVLLLRPGDQVFLQMPSEQAAGLYAGQYVHSSFSGYLLYPM 744
               SCOP domains d1o91c_ C: Collagen NC1 trimerisation domain                                                                                        SCOP domains
               CATH domains 1o91C00 C:613-743  [code=2.60.120.40, no name defined]                                                                              CATH domains
           Pfam domains (1) ---C1q-1o91C01 C:616-740                                                                                                        --- Pfam domains (1)
           Pfam domains (2) ---C1q-1o91C02 C:616-740                                                                                                        --- Pfam domains (2)
           Pfam domains (3) ---C1q-1o91C03 C:616-740                                                                                                        --- Pfam domains (3)
         Sec.struct. author ...eeeeee..............eeeeeehhh.............eeeeeeeeeeeeeeeeeeeeee.................eeeeeeeeeee...............eeee......eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o91 C 613 EMPAFTAELTVPFPPVGAPVKFDKLLYNGRQNYNPQTGIFTCEVPGVYYFAYHVHCKGGNVWVALFKNNEPMMYTYDEYKKGFLDQASGSAVLLLRPGDQVFLQMPSEQAAGLYAGQYVHSSFSGYLLYPM 743
                                   622       632       642       652       662       672       682       692       702       712       722       732       742 

   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, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: C1q_TNF (45)
(-)
Family: C1q (8)
1aC1q-1o91C01C:616-740
1bC1q-1o91C02C:616-740
1cC1q-1o91C03C:616-740

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (CO8A1_MOUSE | Q00780)
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0048593    camera-type eye morphogenesis    The process in which the anatomical structures of the eye are generated and organized. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
    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:0035987    endodermal cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo.
    GO:0050673    epithelial cell proliferation    The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population. Epithelial cells make up the epithelium, the covering of internal and external surfaces of the body, including the lining of vessels and other small cavities. It consists of cells joined by small amounts of cementing substances.
    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: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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    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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