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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE TRIGGERING RECEPTOR EXPRESSED ON MYELOID CELLS 1 (TREM-1) AT 1.76
 
Authors :  M. S. Kelker, E. W. Debler, I. A. Wilson
Date :  09 Aug 04  (Deposition) - 14 Dec 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Activating Receptors, Trem-1, Innate Immunity, Immune System Receptor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. S. Kelker, E. W. Debler, I. A. Wilson
Crystal Structure Of Mouse Triggering Receptor Expressed On Myeloid Cells 1 (Trem-1) At 1. 76A
J. Mol. Biol. V. 344 1175 2004
PubMed-ID: 15561137  |  Reference-DOI: 10.1016/J.JMB.2004.10.009

(-) Compounds

Molecule 1 - TRIGGERING RECEPTOR EXPRESSED ON MYELOID CELLS 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET22B(+)
    Expression System StrainBL21-(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneTREM
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymTRIGGERING RECEPTOR EXPRESSED IN MONOCYTES 1, TREM-1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:33 , ASP A:90 , GLU A:93 , THR A:134BINDING SITE FOR RESIDUE ZN A 135
2AC2SOFTWAREGLU B:33 , ASP B:90 , GLU B:93 , THR B:134BINDING SITE FOR RESIDUE ZN B 135
3AC3SOFTWAREASP A:60 , HIS A:117BINDING SITE FOR RESIDUE ZN A 136

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:41 -A:113
2B:41 -B:113

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Arg A:72 -Pro A:73
2Pro A:118 -Pro A:119
3Arg B:72 -Pro B:73

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U9K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U9K)

(-) Exons   (0, 0)

(no "Exon" information available for 1U9K)

(-) 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:110
 aligned with TREM1_MOUSE | Q9JKE2 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:110
                                    34        44        54        64        74        84        94       104       114       124       134
          TREM1_MOUSE    25 EEERYDLVEGQTLTVKCPFNIMKYANSQKAWQRLPDGKEPLTLVVTQRPFTRPSEVHMGKFTLKHDPSEAMLQVQMTDLQVTDSGLYRCVIYHPPNDPVVLFHPVRLVVT 134
               SCOP domains d1u9ka_ A: TREM-1 (triggering receptor expressed on myeloid cells 1)                                           SCOP domains
               CATH domains 1u9kA00 A:25-134 Immunoglobulins                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeee.hhhhhh..eeeeee.......eeeee........eeeee..eeeeeehhh.eeeeee...hhhhheeeeeeee......ee....eeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1u9k A  25 EEERYDLVEGQTLTVKCPFNIMKYANSQKAWQRLPDGKEPLTLVVTQRPFTRPSEVHMGKFTLKHDPSEAMLQVQMTDLQVTDSGLYRCVIYHPPNDPVVLFHPVRLVVT 134
                                    34        44        54        64        74        84        94       104       114       124       134

Chain B from PDB  Type:PROTEIN  Length:110
 aligned with TREM1_MOUSE | Q9JKE2 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:110
                                    34        44        54        64        74        84        94       104       114       124       134
          TREM1_MOUSE    25 EEERYDLVEGQTLTVKCPFNIMKYANSQKAWQRLPDGKEPLTLVVTQRPFTRPSEVHMGKFTLKHDPSEAMLQVQMTDLQVTDSGLYRCVIYHPPNDPVVLFHPVRLVVT 134
               SCOP domains d1u9kb_ B: TREM-1 (triggering receptor expressed on myeloid cells 1)                                           SCOP domains
               CATH domains 1u9kB00 B:25-134 Immunoglobulins                                                                               CATH domains
           Pfam domains (1) V-set-1u9kB01 B:25-133                                                                                       - Pfam domains (1)
           Pfam domains (2) V-set-1u9kB02 B:25-133                                                                                       - Pfam domains (2)
         Sec.struct. author ..eeeeee....eeeeee.hhhhhh..eeeeee.......eeeee........eeeee..eeeeeehhh.eeeeee...hhhhheeeeeeee......ee....eeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1u9k B  25 EEERYDLVEGQTLTVKCPFNIMKYANSQKAWQRLPDGKEPLTLVVTQRPFTRPSEVHMGKFTLKHDPSEAMLQVQMTDLQVTDSGLYRCVIYHPPNDPVVLFHPVRLVVT 134
                                    34        44        54        64        74        84        94       104       114       124       134

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Ig (577)
(-)
Family: V-set (144)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TREM1_MOUSE | Q9JKE2)
molecular function
    GO:0097110    scaffold protein binding    Interacting selectively and non-covalently with a scaffold protein. Scaffold proteins are crucial regulators of many key signaling pathways. Although not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes.
biological process
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0050755    chemokine metabolic process    The chemical reactions and pathways involving chemokines, any member of a family of small chemotactic cytokines; their name is derived from their ability to induce directed chemotaxis in nearby responsive cells. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria.
    GO:0042107    cytokine metabolic process    The chemical reactions and pathways involving cytokines, any of a group of proteins or glycoproteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity.
    GO:0002374    cytokine secretion involved in immune response    The regulated release of cytokines from a cell that contributes to an immune response.
    GO:0030593    neutrophil chemotaxis    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:0072672    neutrophil extravasation    The migration of a neutrophil from the blood vessels into the surrounding tissue.
    GO:0070945    neutrophil mediated killing of gram-negative bacterium    The directed killing of a gram-negative bacterium by a neutrophil.
    GO:0002230    positive regulation of defense response to virus by host    Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
    GO:0098779    positive regulation of macromitophagy in response to mitochondrial depolarization    The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential.
    GO:0098792    xenophagy    The macroautophagy process in which a region of cytoplasm containing an intracellular pathogen or some part of an intracellular pathogen (e.g. viral capsid) is enclosed in a double membrane bound autophagosome, which then fuses with the lysosome leading to degradation of the contents.
cellular component
    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.

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