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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TIR DOMAIN OF HUMAN TLR1
 
Authors :  Y. Xu, X. Tao, B. Shen, T. Horng, R. Medzhitov, J. L. Manley, L. Tong
Date :  03 Oct 00  (Deposition) - 22 Nov 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Alpha-Beta Fold Parallel Beta Sheet, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Xu, X. Tao, B. Shen, T. Horng, R. Medzhitov, J. L. Manley, L. Tong
Structural Basis For Signal Transduction By The Toll/Interleukin-1 Receptor Domains.
Nature V. 408 111 2000
PubMed-ID: 11081518  |  Reference-DOI: 10.1038/35047056
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TOLL-LIKE RECEPTOR 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentTIR DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1FYV)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:667 -A:686

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_052358L631RTLR1_HUMANPolymorphism5743619AL631R
2UniProtVAR_066346V651ATLR1_HUMANPolymorphism137853174AV651A
3UniProtVAR_066347V674ATLR1_HUMANPolymorphism  ---AV674A
4UniProtVAR_066348H720PTLR1_HUMANPolymorphism113706342AH720P
5UniProtVAR_052359P733LTLR1_HUMANPolymorphism5743621AP733L

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TIRPS50104 TIR domain profile.TLR1_HUMAN635-779  1A:635-779

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3dENST000003089793dENSE00001245751chr4:38806412-3880637538TLR1_HUMAN-00--
1.4aENST000003089794aENSE00001245741chr4:38806003-3880592777TLR1_HUMAN-00--
1.5bENST000003089795bENSE00001245734chr4:38802569-3880247892TLR1_HUMAN-00--
1.6fENST000003089796fENSE00001208820chr4:38800519-387978802640TLR1_HUMAN1-8098091A:625-785161

(-) 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:161
 aligned with TLR1_HUMAN | Q15399 from UniProtKB/Swiss-Prot  Length:786

    Alignment length:161
                                   634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784 
           TLR1_HUMAN   625 NIPLEELQRNLQFHAFISYSGHDSFWVKNELLPNLEKEGMQICLHERNFVPGKSIVENIITCIEKSYKSIFVLSPNFVQSEWCHYELYFAHHNLFHEGSNSLILILLEPIPQYSIPSSYHKLKSLMARRTYLEWPKEKSKRGLFWANLRAAINIKLTEQAK 785
               SCOP domains d1fyva_ A: Toll-like receptor 1, TLR1                                                                                                                             SCOP domains
               CATH domains 1fyvA00 A:625-785  [code=3.40.50.10140, no name defined]                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee.hhhhhhhhhhhhhhhhhh....ee..........hhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhh............eeeee....hhhhh...hhhhhhhhhh...ee...hhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------R-------------------A----------------------A---------------------------------------------P------------L---------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------TIR  PDB: A:635-779 UniProt: 635-779                                                                                                             ------ PROSITE
               Transcript 1 Exon 1.6f  PDB: A:625-785 UniProt: 1-809 [INCOMPLETE]                                                                                                             Transcript 1
                 1fyv A 625 NIPLEELQRNLQFHAFISYSGHDSFWVKNELLPNLEKEGmQICLHERNFVPGKSIVENIITCIEKSYKSIFVLSPNFVQSEWCHYELYFAHHNLFHEGSNSLILILLEPIPQYSIPSSYHKLKSLmARRTYLEWPKEKSKRGLFWANLRAAINIKLTEQAK 785
                                   634       644       654       664       674       684       694       704       714       724       734       744     | 754       764       774       784 
                                                                 664-MSE                                                                               750-MSE                               

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FYV)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TLR1_HUMAN | Q15399)
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:0071723    lipopeptide binding    Interacting selectively and non-covalently with a lipopeptide, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds and containing a nonprotein group consisting of a lipid or lipids.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0004888    transmembrane signaling receptor activity    Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
biological process
    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:0071727    cellular response to triacyl 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 triacylated bacterial lipopeptide stimulus.
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    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:0042495    detection of triacyl bacterial lipopeptide    The series of events in which a triacylated bacterial lipoprotein stimulus is received by a cell and converted into a molecular signal. Triacylated bacterial lipoproteins are lipopeptides of bacterial origin containing a nonprotein moiety consisting of three acyl groups.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    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:0042116    macrophage activation    A change in morphology and behavior of a macrophage resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
    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:0042535    positive regulation of tumor necrosis factor biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of tumor necrosis factor, an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis.
    GO:0050707    regulation of cytokine secretion    Any process that modulates the frequency, rate or extent of the regulated release of cytokines from a cell.
    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:0034130    toll-like receptor 1 signaling pathway    Any series of molecular signals generated as a consequence of binding to toll-like receptor 1.
    GO:0038123    toll-like receptor TLR1:TLR2 signaling pathway    A series of molecular signals initiated by the binding of a heterodimeric TLR1:TLR2 complex to one of it's physiological ligands, followed by transmission of the signal by the activated receptor, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0002224    toll-like receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a toll-like receptor. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0035354    Toll-like receptor 1-Toll-like receptor 2 protein complex    A heterodimeric protein complex containing Toll-like receptor 1 (TLR1) and Toll-like receptor 2 (TLR2).
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0030670    phagocytic vesicle membrane    The lipid bilayer surrounding a phagocytic vesicle.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        TLR1_HUMAN | Q153992z7x

(-) Related Entries Specified in the PDB File

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