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(-) Description

Title :  CRYSTAL STRUCTURE OF MAL ADAPTOR PROTEIN
 
Authors :  E. Valkov, A. Stamp, J. L. Martin, B. Kobe
Date :  11 Feb 11  (Deposition) - 14 Sep 11  (Release) - 19 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.01
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Immune System, Toll-Like Receptor Signaling, Innate Immunity (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Valkov, A. Stamp, F. Dimaio, D. Baker, B. Verstak, P. Roversi, S. Kellie, M. J. Sweet, A. Mansell, N. J. Gay, J. L. Martin, B. Kobe
Crystal Structure Of Toll-Like Receptor Adaptor Mal/Tirap Reveals The Molecular Basis For Signal Transduction And Disease Protection.
Proc. Natl. Acad. Sci. Usa V. 108 14879 2011
PubMed-ID: 21873236  |  Reference-DOI: 10.1073/PNAS.1104780108

(-) Compounds

Molecule 1 - TOLL/INTERLEUKIN-1 RECEPTOR DOMAIN-CONTAINING ADAPTER PROTEIN,
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentTIR DOMAIN, RESIDUES 79-221
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsC91 AND C157 MODIFIED BY DITHIOTHREITOL (DTT)
    SynonymTIR DOMAIN-CONTAINING ADAPTER PROTEIN, ADAPTOR PROTEIN WYATT, MYD88 ADAPTER-LIKE PROTEIN, MAL

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1DTT2Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:91 , HIS A:92 , ARG A:143 , CYS A:157 , GLN A:160BINDING SITE FOR RESIDUE DTT A 300

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:89 -A:134
2A:142 -A:174

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y92)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_019145D96NTIRAP_HUMANPolymorphism8177400AD96N
2UniProtVAR_019146S180LTIRAP_HUMANPolymorphism8177374AS180L
3UniProtVAR_061713V197ITIRAP_HUMANPolymorphism7932976AV197I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_019145D96NTIRAP_HUMANPolymorphism8177400AD96N
2UniProtVAR_019146S180LTIRAP_HUMANPolymorphism8177374AS180L
3UniProtVAR_061713V197ITIRAP_HUMANPolymorphism7932976AV197I

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TIRPS50104 TIR domain profile.TIRAP_HUMAN84-168  1A:84-167
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TIRPS50104 TIR domain profile.TIRAP_HUMAN84-168  2A:84-167

(-) Exons   (0, 0)

(no "Exon" information available for 2Y92)

(-) Sequences/Alignments

Asymmetric 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:127
 aligned with TIRAP_HUMAN | P58753 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:143
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218   
          TIRAP_HUMAN    79 SSRWSKDYDVCVCHSEEDLVAAQDLVSYLEGSTASLRCFLQLRDATPGGAIVSELCQALSSSHCRVLLITPGFLQDPWCKYQMLQALTEAPGAEGCTIPLLSGLSRAAYPPELRFMYYVDGRGPDGGFRQVKEAVMRYLQTLS 221
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.....hhhhhhhhhhhh...------------.......eee......eeeeeeee.hhhhh.hhhhhhhhhhh..----...eeeee.................ee.......hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------N-----------------------------------------------------------------------------------L----------------I------------------------ SAPs(SNPs)
                    PROSITE -----TIR  PDB: A:84-167 UniProt: 84-168                                                   ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y92 A  79 SSRWSKDYDVCVCHSEEDLVAAQDLVSYLEGST------------TPGGAIVSELCQALSSSHCRVLLITPGFLQDPWCKYQMLQALTE----EGCTIPLLSGLSRAAYPPELRFMYYVDGRGPDGGFRQVKEAVMRYLQTLS 221
                                    88        98       108  |      -     | 128       138       148       158        |-   |   178       188       198       208       218   
                                                          111          124                                        167  172                                                 

   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  (0, 0)

(no "SCOP Domain" information available for 2Y92)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y92)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y92)

(-) Gene Ontology  (50, 50)

Asymmetric Unit(hide GO term definitions)
Chain A   (TIRAP_HUMAN | P58753)
molecular function
    GO:0035663    Toll-like receptor 2 binding    Interacting selectively and non-covalently with a Toll-like 2 protein, a pattern recognition receptor that binds microbial pattern motifs to initiate an innate immune response.
    GO:0035662    Toll-like receptor 4 binding    Interacting selectively and non-covalently with a Toll-like 4 protein, a pattern recognition receptor that binds bacterial lipopolysaccharide (LPS) to initiate an innate immune response.
    GO:0005546    phosphatidylinositol-4,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions.
    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:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0005080    protein kinase C binding    Interacting selectively and non-covalently with protein kinase C.
biological process
    GO:0070935    3'-UTR-mediated mRNA stabilization    An mRNA stabilization process in which one or more RNA-binding proteins associate with the 3'-untranslated region (UTR) of an mRNA.
    GO:0002755    MyD88-dependent toll-like receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the MyD88 adaptor molecule mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
    GO:0035665    TIRAP-dependent toll-like receptor 4 signaling pathway    Any series of molecular signals generated as a consequence of binding to a toll-like receptor 4 where the TIRAP/MAL adaptor mediates transduction of the signal. Toll-like 4 receptors are pattern recognition receptors that bind bacterial lipopolysaccharide (LPS) to initiate an innate immune response.
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0071221    cellular response to bacterial lipopeptide    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 bacterial lipopeptide stimulus.
    GO:0071223    cellular response to lipoteichoic acid    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 lipoteichoic acid stimulus; lipoteichoic acid is a major component of the cell wall of gram-positive bacteria and typically consists of a chain of glycerol-phosphate repeating units linked to a glycolipid anchor.
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium 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:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0030099    myeloid cell differentiation    The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages.
    GO:0044130    negative regulation of growth of symbiont in host    Any process in which the symbiont stops, prevents or reduces its increase in size or mass within the cells or tissues of the host organism. The host is defined as the larger of the organisms involved in the symbiotic interaction.
    GO:0030890    positive regulation of B cell proliferation    Any process that activates or increases the rate or extent of B cell proliferation.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0046330    positive regulation of JNK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the JNK cascade.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:2000340    positive regulation of chemokine (C-X-C motif) ligand 1 production    Any process that activates or increases the frequency, rate or extent of chemokine (C-X-C motif) ligand 1 production.
    GO:2000343    positive regulation of chemokine (C-X-C motif) ligand 2 production    Any process that activates or increases the frequency, rate or extent of chemokine (C-X-C motif) ligand 2 production.
    GO:0032735    positive regulation of interleukin-12 production    Any process that activates or increases the frequency, rate, or extent of interleukin-12 production.
    GO:0032738    positive regulation of interleukin-15 production    Any process that activates or increases the frequency, rate, or extent of interleukin-15 production.
    GO:0045410    positive regulation of interleukin-6 biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-6.
    GO:0032757    positive regulation of interleukin-8 production    Any process that activates or increases the frequency, rate, or extent of interleukin-8 production.
    GO:0090023    positive regulation of neutrophil chemotaxis    Any process that increases the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0090073    positive regulation of protein homodimerization activity    Any process that increases the frequency, rate or extent of protein homodimerization, interacting selectively with an identical protein to form a homodimer.
    GO:0034137    positive regulation of toll-like receptor 2 signaling pathway    Any process that activates or increases the frequency, rate, or extent of toll-like receptor 2 signaling pathway.
    GO:0034141    positive regulation of toll-like receptor 3 signaling pathway    Any process that activates or increases the frequency, rate, or extent of toll-like receptor 3 signaling pathway.
    GO:0034145    positive regulation of toll-like receptor 4 signaling pathway    Any process that activates or increases the frequency, rate, or extent of toll-like receptor 4 signaling pathway.
    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:0045088    regulation of innate immune response    Any process that modulates the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection.
    GO:0032648    regulation of interferon-beta production    Any process that modulates the frequency, rate, or extent of interferon-beta 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.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0034142    toll-like receptor 4 signaling pathway    Any series of molecular signals generated as a consequence of binding to toll-like receptor 4.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030139    endocytic vesicle    A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
    GO:0045171    intercellular bridge    A direct connection between the cytoplasm of two cells that is formed following the completion of cleavage furrow ingression during cell division. They are usually present only briefly prior to completion of cytokinesis. However, in some cases, such as the bridges between germ cells during their development, they become stabilised.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.
    GO:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TIRAP_HUMAN | P587532ndh 3ub2 3ub3 3ub4 4fz5 4lqd 5t7q

(-) Related Entries Specified in the PDB File

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