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(-) Description

Title :  CRYSTAL STRUCTURE OF THE IG V-SET DOMAIN OF HUMAN PAIRED IMMUNOGLOBULIN-LIKE TYPE 2 RECEPTOR ALPHA
 
Authors :  K. Kuroki, J. Wang, T. Ose, M. Yamaguchi, S. Tabata, N. Maita, S. Nakamur M. Kajikawa, A. Kogure, T. Satoh, H. Arase, K. Maenaka
Date :  10 May 14  (Deposition) - 11 Jun 14  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Immunoglobulin-Like, Immunological Receptor, Membrane, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Kuroki, J. Wang, T. Ose, M. Yamaguchi, S. Tabata, N. Maita, S. Nakamura, M. Kajikawa, A. Kogure, T. Satoh, H. Arase, K. Maenaka
Structural Basis For Simultaneous Recognition Of An O-Glyca And Its Attached Peptide Of Mucin Family By Immune Receptor Pilr Alpha
Proc. Natl. Acad. Sci. Usa V. 111 8877 2014
PubMed-ID: 24889612  |  Reference-DOI: 10.1073/PNAS.1324105111

(-) Compounds

Molecule 1 - PAIRED IMMUNOGLOBULIN-LIKE TYPE 2 RECEPTOR ALPHA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGMT7
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentV-SET DOMAIN, UNP RESIDUES 32-150
    GenePILRA
    MutationYES
    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  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2IPA1Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:101 , GLY A:104 , GLN A:105BINDING SITE FOR RESIDUE IPA A 201
2AC2SOFTWAREMET A:31 , GLU A:50 , ARG A:73 , GLY A:74 , HIS A:75 , PHE A:76 , HIS A:77 , GLY A:78 , GLN A:79 , HOH A:364 , HOH A:368 , HOH A:371BINDING SITE FOR RESIDUE CIT A 202
3AC3SOFTWAREGLN A:37 , LYS A:39 , TRP A:59 , GLU A:60 , ARG A:72 , GLN A:79 , SER A:80 , HOH A:315 , HOH A:317 , HOH A:332 , HOH A:349 , HOH A:362BINDING SITE FOR RESIDUE CIT A 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WUZ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:85 -Pro A:86

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_060361R78GPILRA_HUMANPolymorphism1859788AG78G

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WUZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3WUZ)

(-) 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:120
 aligned with C9JGG1_HUMAN | C9JGG1 from UniProtKB/TrEMBL  Length:166

    Alignment length:120
                                    40        50        60        70        80        90       100       110       120       130       140       150
         C9JGG1_HUMAN    31 YLYGVTQPKHLSASMGGSVEIPFSFYYPWELATAPDVRISWRRGHFHRQSFYSTRPPSIHKDYVNRLFLNWTEGQKSGFLRISNLQKQDQSVYFCRVELDTRSSGRQQWQSIEGTKLSIT 150
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee...eeeee....eeeeeeee...........eeeeeee....eeeee....ee.hhhh..eeee......eeeeee...hhhhheeeeeeeeeee...eeeeee....eeeeee Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------G------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3wuz A  31 MLYGVTQPKHLSASMGGSVEIPFSFYYPWELATAPDVRISWRRGHFHGQSFYSTRPPSIHKDYVNRLFLNWTEGQKSGFLRISNLQKQDQSVYFCRVELDTRSSGRQQWQSIEGTKLSIT 150
                                    40        50        60        70        80        90       100       110       120       130       140       150

Chain A from PDB  Type:PROTEIN  Length:120
 aligned with PILRA_HUMAN | Q9UKJ1 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:120
                                    40        50        60        70        80        90       100       110       120       130       140       150
          PILRA_HUMAN    31 YLYGVTQPKHLSASMGGSVEIPFSFYYPWELATAPDVRISWRRGHFHRQSFYSTRPPSIHKDYVNRLFLNWTEGQKSGFLRISNLQKQDQSVYFCRVELDTRSSGRQQWQSIEGTKLSIT 150
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee...eeeee....eeeeeeee...........eeeeeee....eeeee....ee.hhhh..eeee......eeeeee...hhhhheeeeeeeeeee...eeeeee....eeeeee Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------G------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3wuz A  31 MLYGVTQPKHLSASMGGSVEIPFSFYYPWELATAPDVRISWRRGHFHGQSFYSTRPPSIHKDYVNRLFLNWTEGQKSGFLRISNLQKQDQSVYFCRVELDTRSSGRQQWQSIEGTKLSIT 150
                                    40        50        60        70        80        90       100       110       120       130       140       150

   Legend:   → Mismatch (orange background)
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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 3WUZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WUZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WUZ)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (C9JGG1_HUMAN | C9JGG1)

Chain A   (PILRA_HUMAN | Q9UKJ1)
molecular function
    GO:0042288    MHC class I protein binding    Interacting selectively and non-covalently with major histocompatibility complex class I molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation.
    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).
biological process
    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:0007169    transmembrane receptor protein tyrosine kinase signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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: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
        C9JGG1_HUMAN | C9JGG13wv0
        PILRA_HUMAN | Q9UKJ13wv0 4nfb

(-) Related Entries Specified in the PDB File

3wv0