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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TOLL/INTERLEUKIN-1 RECEPTOR (TIR) DOMAIN OF HUMAN IL-1RAPL
 
Authors :  J. A. Khan, L. Tong
Date :  26 Apr 04  (Deposition) - 08 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tir, Il-1Rapl, Il-1R, Tlr, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. A. Khan, E. K. Brint, L. A. J. O'Neill, L. Tong
Crystal Structure Of The Toll/Interleukin-1 Receptor Domain Of Human Il-1Rapl
J. Biol. Chem. V. 279 31664 2004
PubMed-ID: 15123616  |  Reference-DOI: 10.1074/JBC.M403434200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - X-LINKED INTERLEUKIN-1 RECEPTOR ACCESSORY PROTEIN-LIKE 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET26B
    Expression System StrainDL41(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentTIR
    GeneIL1RAPL1, OPHN4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIL1RAPL-1, OLIGOPHRENIN-4, THREE IMMUNOGLOBULIN DOMAIN-CONTAINING IL-1 RECEPTOR-RELATED 2, TIGIRR-2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1T3G)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T3G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1T3G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T3G)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TIRPS50104 TIR domain profile.IRPL1_HUMAN403-562
 
  2A:403-561
B:403-561

(-) Exons   (2, 4)

Asymmetric/Biological Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003789931ENSE00001479491X:28605516-28606164649IRPL1_HUMAN-00--
1.2aENST000003789932aENSE00001479488X:28807437-28807542106IRPL1_HUMAN1-28280--
1.3ENST000003789933ENSE00001325615X:29301055-29301334280IRPL1_HUMAN28-121940--
1.4ENST000003789934ENSE00001013358X:29414375-29414561187IRPL1_HUMAN121-183630--
1.5ENST000003789935ENSE00001013357X:29417272-29417425154IRPL1_HUMAN184-235520--
1.6ENST000003789936ENSE00001330704X:29686547-2968662175IRPL1_HUMAN235-260260--
1.7ENST000003789937ENSE00001161148X:29935581-29935713133IRPL1_HUMAN260-304450--
1.8ENST000003789938ENSE00001161138X:29938066-29938211146IRPL1_HUMAN304-353500--
1.9ENST000003789939ENSE00001161126X:29959768-29959911144IRPL1_HUMAN353-401490--
1.10ENST0000037899310ENSE00001161119X:29972639-29972809171IRPL1_HUMAN401-458582A:403-458 (gaps)
B:403-458 (gaps)
56
56
1.11bENST0000037899311bENSE00001479458X:29973219-299748401622IRPL1_HUMAN458-6962392A:458-561
B:458-561
104
104

(-) 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:152
 aligned with IRPL1_HUMAN | Q9NZN1 from UniProtKB/Swiss-Prot  Length:696

    Alignment length:159
                                   412       422       432       442       452       462       472       482       492       502       512       522       532       542       552         
          IRPL1_HUMAN   403 KDYDAYLSYTKVDPDQWNQETGEEERFALEILPDMLEKHYGYKLFIPDRDLIPTGTYIEDVARCVDQSKRLIIVMTPNYVVRRGWSIFELETRLRNMLVTGEIKVILIECSELRGIMNYQEVEALKHTIKLLTVIKWHGPKCNKLNSKFWKRLQYEMPF 561
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1t3gA00 A:403       -561  [code=3.40.50.10140, no name defined]                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.....-------..hhhhhhhhhhhhhhhhh....eehhhhhh....hhhhhhhhhhhh..eeeeeehhhhhhh..hhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhh...eeeee..hhhhhh..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE TIR  PDB: A:403-561 UniProt: 403-562                                                                                                                            PROSITE
           Transcript 1 (1) Exon 1.10  PDB: A:403-458 (gaps) UniProt: 401-458       ------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------Exon 1.11b  PDB: A:458-561 UniProt: 458-696 [INCOMPLETE]                                                 Transcript 1 (2)
                 1t3g A 403 KDYDAYLSYTKVD-------TGEEERFALEILPDmLEKHYGYKLFIPDRDLIPTGTYIEDVARCVDQSKRLIIVmTPNYVVRRGWSIFELETRLRNmLVTGEIKVILIECSELRGImNYQEVEALKHTIKLLTVIKWHGPKCNKLNSKFWKRLQYEmPF 561
                                   412  |      -|      432    |  442       452       462       472    |  482       492      |502       512      |522       532       542       552      |  
                                      415     423           437-MSE                                 477-MSE               499-MSE             519-MSE                                 559-MSE

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with IRPL1_HUMAN | Q9NZN1 from UniProtKB/Swiss-Prot  Length:696

    Alignment length:159
                                   412       422       432       442       452       462       472       482       492       502       512       522       532       542       552         
          IRPL1_HUMAN   403 KDYDAYLSYTKVDPDQWNQETGEEERFALEILPDMLEKHYGYKLFIPDRDLIPTGTYIEDVARCVDQSKRLIIVMTPNYVVRRGWSIFELETRLRNMLVTGEIKVILIECSELRGIMNYQEVEALKHTIKLLTVIKWHGPKCNKLNSKFWKRLQYEMPF 561
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1t3gB00 B:40        3-561  [code=3.40.50.10140, no name defined]                                                                                                CATH domains
           Pfam domains (1) ----TIR-1t3g        B01 B:407-558                                                                                                                           --- Pfam domains (1)
           Pfam domains (2) ----TIR-1t3g        B02 B:407-558                                                                                                                           --- Pfam domains (2)
         Sec.struct. author ....eeee....--------.hhhhhhhhhhhhhhhhhh....eehhhhhh....hhhhhhhhhhhh...eeeeehhhhhhhh.hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh....eeeee..hhhhhh..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE TIR  PDB: B:403-561 UniProt: 403-562                                                                                                                            PROSITE
           Transcript 1 (1) Exon 1.10  PDB: B:403-458 (gaps) UniProt: 401-458       ------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------Exon 1.11b  PDB: B:458-561 UniProt: 458-696 [INCOMPLETE]                                                 Transcript 1 (2)
                 1t3g B 403 KDYDAYLSYTKV--------TGEEERFALEILPDmLEKHYGYKLFIPDRDLIPTGTYIEDVARCVDQSKRLIIVmTPNYVVRRGWSIFELETRLRNmLVTGEIKVILIECSELRGImNYQEVEALKHTIKLLTVIKWHGPKCNKLNSKFWKRLQYEmPF 561
                                   412 |       -|      432    |  442       452       462       472    |  482       492      |502       512      |522       532       542       552      |  
                                     414      423           437-MSE                                 477-MSE               499-MSE             519-MSE                                 559-MSE

   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 1T3G)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: STIR (4)
(-)
Family: TIR (4)
1aTIR-1t3gB01B:407-558
1bTIR-1t3gB02B:407-558

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (IRPL1_HUMAN | Q9NZN1)
molecular function
    GO:0019966    interleukin-1 binding    Interacting selectively and non-covalently with interleukin-1.
    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:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0005245    voltage-gated calcium channel activity    Enables the transmembrane transfer of a calcium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
    GO:0070588    calcium ion transmembrane transport    A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0007157    heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules    The attachment of an adhesion molecule in one cell to a nonidentical adhesion molecule in an adjacent cell.
    GO:0045920    negative regulation of exocytosis    Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis.
    GO:0030182    neuron differentiation    The process in which a relatively unspecialized cell acquires specialized features of a neuron.
    GO:0050775    positive regulation of dendrite morphogenesis    Any process that activates or increases the frequency, rate or extent of dendrite morphogenesis.
    GO:0097105    presynaptic membrane assembly    The aggregation, arrangement and bonding together of a set of components to form a presynaptic membrane, including any proteins associated with the membrane, but excluding other cellular components. A presynaptic membrane is a specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction.
    GO:0010975    regulation of neuron projection development    Any process that modulates the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    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.
cellular component
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    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: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.
    GO:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IRPL1_HUMAN | Q9NZN14m92

(-) Related Entries Specified in the PDB File

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