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(-) Description

Title :  STRUCTURE OF THE F-SPONDIN DOMAIN OF MINDIN
 
Authors :  Y. Li, R. A. Mariuzza
Date :  09 May 08  (Deposition) - 17 Feb 09  (Release) - 17 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  F-Spondin Domain Of Mindin, Cell Adhesion, Extracellular Matrix, Immune Response, Polymorphism, Secreted, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Li, C. Cao, W. Jia, L. Yu, M. Mo, Q. Wang, Y. Huang, J. M. Lim, M. Ishihara, L. Wells, P. Azadi, H. Robinson, Y. W. He, L. Zhang, R. A. Mariuzza
Structure Of The F-Spondin Domain Of Mindin, An Integrin Ligand And Pattern Recognition Molecule.
Embo J. V. 28 286 2009
PubMed-ID: 19153605  |  Reference-DOI: 10.1038/EMBOJ.2008.288
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SPONDIN-2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentF-SPONDIN DOMAIN, UNP RESIDUES 27-249
    GeneSPON2, DIL1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMINDIN, DIFFERENTIALLY EXPRESSED IN CANCEROUS AND NON-CANCEROUS LUNG CELLS 1, DIL-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2NI6Ligand/IonNICKEL (II) ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:175BINDING SITE FOR RESIDUE NI A 224
2AC2SOFTWARELYS B:16BINDING SITE FOR RESIDUE NI B 224
3AC3SOFTWAREGLU A:96BINDING SITE FOR RESIDUE NI A 225
4AC4SOFTWARELYS A:16BINDING SITE FOR RESIDUE NI A 226
5AC5SOFTWARELYS B:16 , GLU B:96BINDING SITE FOR RESIDUE NI B 225
6AC7SOFTWAREASP A:134 , ASP A:162 , ASP A:166BINDING SITE FOR RESIDUE CA A 228
7AC8SOFTWAREASP B:134 , ASP B:162 , ASP B:166BINDING SITE FOR RESIDUE CA B 226

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:9 -A:145
2B:9 -B:145

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Arg A:38 -Pro A:39
2Val A:130 -Pro A:131
3Ile A:179 -Pro A:180
4Ser A:191 -Pro A:192
5Arg B:38 -Pro B:39
6Val B:130 -Pro B:131
7Ile B:179 -Pro B:180
8Ser B:191 -Pro B:192

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 8)

Asymmetric/Biological Unit (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_055149R38GSPON2_HUMANPolymorphism6836335A/BR12G
2UniProtVAR_019701L40PSPON2_HUMANPolymorphism922697A/BP14P
3UniProtVAR_019702E122ASPON2_HUMANPolymorphism11247975A/BE96A
4UniProtVAR_019703V242LSPON2_HUMANPolymorphism2279279A/BL216L

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D34)

(-) Exons   (0, 0)

(no "Exon" information available for 3D34)

(-) 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:211
 aligned with SPON2_HUMAN | Q9BUD6 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:211
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243 
          SPON2_HUMAN    34 ICSARALAKYSITFTGKWSQTAFPKQYPLFRPPAQWSSLLGAAHSSDYSMWRKNQYVSNGLRDFAERGEAWALMKEIEAAGEALQSVHEVFSAPAVPSGTGQTSAELEVQRRHSLVSFVVRIVPSPDWFVGVDSLDLCDGDRWREQAALDLYPYDAGTDSGFTFSSPNFATIPQDTVTEITSSSPSHPANSFYYPRLKALPPIARVTLVRL 244
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee..................eeeeeeeeee.............hhhhhhhhhhh.hhhhhhhhhhhhhhhh.eeeeeee........eeeeeeee.....eeeeeeeee....eeeeeeeee.ee..ee..eeeeee..ee......................ee........................eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----G-P---------------------------------------------------------------------------------A-----------------------------------------------------------------------------------------------------------------------L-- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d34 A   8 ICSARAPAKYSITFTGKWSQTAFPKQYPLFRPPAQWSSLLGAAHSSDYSMWRKNQYVSNGLRDFAERGEAWALMKEIEAAGEALQSVHEVFSAPAVPSGTGQTSAELEVQRRHSLVSFVVRIVPSPDWFVGVDSLDLCDGDRWREQAALDLYPYDAGTDSGFTFSSPNFATIPQDTVTEITSSSPSHPANSFYYPRLKALPPIARVTLLRL 218
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217 

Chain B from PDB  Type:PROTEIN  Length:215
 aligned with SPON2_HUMAN | Q9BUD6 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:215
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243     
          SPON2_HUMAN    34 ICSARALAKYSITFTGKWSQTAFPKQYPLFRPPAQWSSLLGAAHSSDYSMWRKNQYVSNGLRDFAERGEAWALMKEIEAAGEALQSVHEVFSAPAVPSGTGQTSAELEVQRRHSLVSFVVRIVPSPDWFVGVDSLDLCDGDRWREQAALDLYPYDAGTDSGFTFSSPNFATIPQDTVTEITSSSPSHPANSFYYPRLKALPPIARVTLVRLRQSP 248
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee.................ee..eeeeee.............hhhhhhhhhhh.hhhhhhhhhhhhhhhh.eeeeeee......eeeeeeeeee.....eeeeeeeee....eeeeeeeee.ee..ee..eeeeee..ee......................ee........................eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----G-P---------------------------------------------------------------------------------A-----------------------------------------------------------------------------------------------------------------------L------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d34 B   8 ICSARAPAKYSITFTGKWSQTAFPKQYPLFRPPAQWSSLLGAAHSSDYSMWRKNQYVSNGLRDFAERGEAWALMKEIEAAGEALQSVHEVFSAPAVPSGTGQTSAELEVQRRHSLVSFVVRIVPSPDWFVGVDSLDLCDGDRWREQAALDLYPYDAGTDSGFTFSSPNFATIPQDTVTEITSSSPSHPANSFYYPRLKALPPIARVTLLRLRQSP 222
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217     

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3D34)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3D34)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D34)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SPON2_HUMAN | Q9BUD6)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
    GO:0001530    lipopolysaccharide binding    Interacting selectively and non-covalently with lipopolysaccharide.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
biological process
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    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:0071222    cellular response to lipopolysaccharide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0050832    defense response to fungus    Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0043152    induction of bacterial agglutination    Any process in which infecting bacteria are clumped together by a host organism.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0002448    mast cell mediated immunity    Any process involved in the carrying out of an immune response by a mast cell.
    GO:0008228    opsonization    The process in which a microorganism (or other particulate material) is rendered more susceptible to phagocytosis by coating with an opsonin, a blood serum protein such as a complement component or antibody.
    GO:0032755    positive regulation of interleukin-6 production    Any process that activates or increases the frequency, rate, or extent of interleukin-6 production.
    GO:0060907    positive regulation of macrophage cytokine production    Any process that increases the rate, frequency or extent of macrophage cytokine production. Macrophage cytokine production is the appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0032760    positive regulation of tumor necrosis factor production    Any process that activates or increases the frequency, rate, or extent of tumor necrosis factor production.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
cellular component
    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: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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