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(-) Description

Title :  ASSEMBLY DOMAIN OF CARTILAGE OLIGOMERIC MATRIX PROTEIN
 
Authors :  V. N. Malashkevich
Date :  12 Sep 96  (Deposition) - 08 Oct 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Extracellular Matrix Protein, Assembly Domain, Cartilage, Oligomeric Matrix Protein, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. N. Malashkevich, R. A. Kammerer, V. P. Efimov, T. Schulthess, J. Engel
The Crystal Structure Of A Five-Stranded Coiled Coil In Comp: A Prototype Ion Channel?
Science V. 274 761 1996
PubMed-ID: 8864111  |  Reference-DOI: 10.1126/SCIENCE.274.5288.761
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARTILAGE OLIGOMERIC MATRIX PROTEIN
    Cell LineBL21
    ChainsA, B, C, D, E
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-3B
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    FragmentASSEMBLY DOMAIN
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    Other DetailsPENTAMERIC COILED-COIL
    SynonymCOMP
    TissueCARTILAGE

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit ABCDE

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:54 , GLN B:54 , GLN C:54 , GLN D:54 , GLN E:54BINDING SITE FOR RESIDUE CL A 500
2IONUNKNOWNGLN A:54 , GLN B:54 , GLN C:54 , GLN D:54 , GLN E:54BINDS CL-.

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:68 -E:71
2A:71 -B:68
3B:71 -C:68
4C:71 -D:68
5D:71 -E:68

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VDF)

(-) 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:46
 aligned with COMP_RAT | P35444 from UniProtKB/Swiss-Prot  Length:755

    Alignment length:46
                                    36        46        56        66      
              COMP_RAT   27 GDLAPQMLRELQETNAALQDVRELLRHRVKEITFLKNTVMECDACG 72
               SCOP domains d1vdfa_ A:                                     SCOP domains
               CATH domains 1vdfA00 A:27-72                                CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                  1vdf A 27 MDLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDACG 72
                                    36        46        56        66      

Chain B from PDB  Type:PROTEIN  Length:46
 aligned with COMP_RAT | P35444 from UniProtKB/Swiss-Prot  Length:755

    Alignment length:46
                                    36        46        56        66      
              COMP_RAT   27 GDLAPQMLRELQETNAALQDVRELLRHRVKEITFLKNTVMECDACG 72
               SCOP domains d1vdfb_ B:                                     SCOP domains
               CATH domains 1vdfB00 B:27-72                                CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                  1vdf B 27 MDLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDACG 72
                                    36        46        56        66      

Chain C from PDB  Type:PROTEIN  Length:46
 aligned with COMP_RAT | P35444 from UniProtKB/Swiss-Prot  Length:755

    Alignment length:46
                                    36        46        56        66      
              COMP_RAT   27 GDLAPQMLRELQETNAALQDVRELLRHRVKEITFLKNTVMECDACG 72
               SCOP domains d1vdfc_ C:                                     SCOP domains
               CATH domains 1vdfC00 C:27-72                                CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                  1vdf C 27 MDLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDACG 72
                                    36        46        56        66      

Chain D from PDB  Type:PROTEIN  Length:46
 aligned with COMP_RAT | P35444 from UniProtKB/Swiss-Prot  Length:755

    Alignment length:46
                                    36        46        56        66      
              COMP_RAT   27 GDLAPQMLRELQETNAALQDVRELLRHRVKEITFLKNTVMECDACG 72
               SCOP domains d1vdfd_ D:                                     SCOP domains
               CATH domains 1vdfD00 D:27-72                                CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                  1vdf D 27 MDLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDACG 72
                                    36        46        56        66      

Chain E from PDB  Type:PROTEIN  Length:46
 aligned with COMP_RAT | P35444 from UniProtKB/Swiss-Prot  Length:755

    Alignment length:46
                                    36        46        56        66      
              COMP_RAT   27 GDLAPQMLRELQETNAALQDVRELLRHRVKEITFLKNTVMECDACG 72
               SCOP domains d1vdfe_ E:                                     SCOP domains
               CATH domains 1vdfE00 E:27-72                                CATH domains
           Pfam domains (1) -COMP-1vdfE01 E:28-72                          Pfam domains (1)
           Pfam domains (2) -COMP-1vdfE02 E:28-72                          Pfam domains (2)
           Pfam domains (3) -COMP-1vdfE03 E:28-72                          Pfam domains (3)
           Pfam domains (4) -COMP-1vdfE04 E:28-72                          Pfam domains (4)
           Pfam domains (5) -COMP-1vdfE05 E:28-72                          Pfam domains (5)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                  1vdf E 27 MDLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDACG 72
                                    36        46        56        66      

   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, 5)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 5)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 5)

Asymmetric/Biological Unit
(-)
Family: COMP (2)
1aCOMP-1vdfE01E:28-72
1bCOMP-1vdfE02E:28-72
1cCOMP-1vdfE03E:28-72
1dCOMP-1vdfE04E:28-72
1eCOMP-1vdfE05E:28-72

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E   (COMP_RAT | P35444)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0005201    extracellular matrix structural constituent    The action of a molecule that contributes to the structural integrity of the extracellular matrix.
    GO:0001968    fibronectin binding    Interacting selectively and non-covalently with a fibronectin, a group of related adhesive glycoproteins of high molecular weight found on the surface of animal cells, connective tissue matrices, and in extracellular fluids.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0005499    vitamin D binding    Interacting selectively and non-covalently with vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3).
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    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: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.
cellular component
    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

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        COMP_RAT | P354441fbm

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