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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF HUMAN NLRP10/PYNOD PYRIN DOMAIN
 
Authors :  M. Y. Su, C. F. Chang, C. I. Chang
Date :  11 Mar 13  (Deposition) - 03 Apr 13  (Release) - 31 Jul 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Nlrp10, Pynod, Pyrin Domain, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Y. Su, C. I. Kuo, C. F. Chang, C. I. Chang
Three-Dimensional Structure Of Human Nlrp10/Pynod Pyrin Domain Reveals A Homotypic Interaction Site Distinct From Its Mouse Homologue.
Plos One V. 8 67843 2013
PubMed-ID: 23861819  |  Reference-DOI: 10.1371/JOURNAL.PONE.0067843
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NACHT, LRR AND PYD DOMAINS-CONTAINING PROTEIN 10
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM11
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-100
    Gene: NLRP10, NALP10, NOD8, PYNOD
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NUCLEOTIDE-BINDING OLIGOMERIZATION DOMAIN PROTEIN 8

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2M5V)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DAPINPS50824 DAPIN domain profile.NAL10_HUMAN3-96  1A:5-98
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DAPINPS50824 DAPIN domain profile.NAL10_HUMAN3-96  1A:5-98

(-) Exons   (0, 0)

(no "Exon" information available for 2M5V)

(-) Sequences/Alignments

NMR Structure
   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:102
 aligned with NAL10_HUMAN | Q86W26 from UniProtKB/Swiss-Prot  Length:655

    Alignment length:102
                              1                                                                                                   
                              |      8        18        28        38        48        58        68        78        88        98  
          NAL10_HUMAN     - --MAMAKARKPREALLWALSDLEENDFKKLKFYLRDMTLSEGQPPLARGELEGLIPVDLAELLISKYGEKEAVKVVLKGLKVMNLLELVDQLSHICLHDYRE 100
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----DAPIN  PDB: A:5-98 UniProt: 3-96                                                              ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2m5v A   1 GAMAMAKARKPREALLWALSDLEENDFKKLKFYLRDMTLSEGQPPLARGELEGLIPVDLAELLISKYGEKEAVKVVLKGLKVMNLLELVDQLSHICLHDYRE 102
                                    10        20        30        40        50        60        70        80        90       100
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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 2M5V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2M5V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2M5V)

(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A   (NAL10_HUMAN | Q86W26)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    GO:0050829    defense response to Gram-negative bacterium    Reactions triggered in response to the presence of a Gram-negative 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:0036336    dendritic cell migration    The movement of a dendritic cell within or between different tissues and organs of the body.
    GO:0035397    helper T cell enhancement of adaptive immune response    Positive regulation of an adaptive immune response mediated via cytokine production by helper T cell.
    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:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0002827    positive regulation of T-helper 1 type immune response    Any process that activates or increases the frequency, rate, or extent of a T-helper 1 type immune response.
    GO:2000318    positive regulation of T-helper 17 type immune response    Any process that activates or increases the frequency, rate or extent of T-helper 17 type immune response.
    GO:2000778    positive regulation of interleukin-6 secretion    Any process that activates or increases the frequency, rate or extent of interleukin-6 secretion.
    GO:2000484    positive regulation of interleukin-8 secretion    Any process that activates or increases the frequency, rate or extent of interleukin-8 secretion.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0019897    extrinsic component of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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