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(-) Description

Title :  CRYSTAL STRUCTURE OF INTERLEUKIN 15 IN COMPLEX WITH INTERLEUKIN 15 RECEPTOR ALPHA
 
Authors :  S. K. Olsen, K. Murayama, S. Kishishita, M. Kukimoto-Niino, T. Terada, M. Shirouzu, N. Ota, O. Kanagawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  07 May 07  (Deposition) - 06 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym. Unit :  A,B,C,F
Biol. Unit 1:  A,F  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Cytokine, Glycoprotein, Secreted, Alternative Splicing, Endoplasmic Reticulum, Golgi Apparatus, Membrane, Nucleus, Phosphorylation, Receptor, Sushi, Transmembrane, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. K. Olsen, N. Ota, S. Kishishita, M. Kukimoto-Niino, K. Murayama, H. Uchiyama, M. Toyama, T. Terada, M. Shirouzu, O. Kanagawa, S. Yokoyama
Crystal Structure Of The Interleukin-15{Middle Dot}Interleukin-15 Receptor {Alpha} Complex: Insights Into Trans And Cis Presentation
J. Biol. Chem. V. 282 37191 2007
PubMed-ID: 17947230  |  Reference-DOI: 10.1074/JBC.M706150200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTERLEUKIN-15
    ChainsA, B
    EngineeredYES
    Expression System Vector TypePLASMID
    GeneIL15
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsCELL FREE EXPRESSION: E.COLI
    SynonymIL-15
 
Molecule 2 - INTERLEUKIN-15 RECEPTOR ALPHA CHAIN
    ChainsF, C
    EngineeredYES
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 33-103
    GeneIL15RA
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsCELL FREE EXPRESSION: E.COLI
    SynonymIL-15R-ALPHA, IL- 15RA

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCF
Biological Unit 1 (1x)A  F
Biological Unit 2 (1x) BC 

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1BAM1Ligand/IonBENZAMIDINE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1BAM-1Ligand/IonBENZAMIDINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BAM1Ligand/IonBENZAMIDINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:4 , TYR A:7 , GLY B:0 , ASP B:4 , TYR B:7BINDING SITE FOR RESIDUE BAM B 115

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:35 -A:85
2A:42 -A:88
3B:35 -B:85
4B:42 -B:88
5C:4 -C:46
6C:30 -C:64
7F:4 -F:46
8F:30 -F:64

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PSM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PSM)

(-) Exons   (0, 0)

(no "Exon" information available for 2PSM)

(-) 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:117
 aligned with IL15_MOUSE | P48346 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:117
                                    55        65        75        85        95       105       115       125       135       145       155       
           IL15_MOUSE    46 TEANWIDVRYDLEKIESLIQSIHIDTTLYTDSDFHPSCKVTAMNCFLLELQVILHEYSNMTLNETVRNVLYLANSTLSSNKNVAESGCKECEELEEKTFTEFLQSFIRIVQMFINTS 162
               SCOP domains ---d2psma1 A:1-114 Interleukin-15 (IL-15)                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.........hhhhheeeehhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2psm A  -2 SSGNWIDVRYDLEKIESLIQSIHIDTTLYTDSDFHPSCKVTAMNCFLLELQVILHEYSNMTLNETVRNVLYLANSTLSSNKNVAESGCKECEELEEKTFTEFLQSFIRIVQMFINTS 114
                                     7        17        27        37        47        57        67        77        87        97       107       

Chain B from PDB  Type:PROTEIN  Length:117
 aligned with IL15_MOUSE | P48346 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:117
                                    55        65        75        85        95       105       115       125       135       145       155       
           IL15_MOUSE    46 TEANWIDVRYDLEKIESLIQSIHIDTTLYTDSDFHPSCKVTAMNCFLLELQVILHEYSNMTLNETVRNVLYLANSTLSSNKNVAESGCKECEELEEKTFTEFLQSFIRIVQMFINTS 162
               SCOP domains d2psmb_ B: Interleukin-15 (IL-15)                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---IL15-2psmB01 B:1-112                                                                                            -- Pfam domains (1)
           Pfam domains (2) ---IL15-2psmB02 B:1-112                                                                                            -- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.........hhhhh.eeehhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2psm B  -2 SSGNWIDVRYDLEKIESLIQSIHIDTTLYTDSDFHPSCKVTAMNCFLLELQVILHEYSNMTLNETVRNVLYLANSTLSSNKNVAESGCKECEELEEKTFTEFLQSFIRIVQMFINTS 114
                                     7        17        27        37        47        57        67        77        87        97       107       

Chain C from PDB  Type:PROTEIN  Length:69
 aligned with I15RA_MOUSE | Q60819 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:69
                                    44        54        64        74        84        94         
          I15RA_MOUSE    35 TCPPPVSIEHADIRVKNYSVNSRERYVCNSGFKRKAGTSTLIECVINKNTNVAHWTTPSLKCIRDPSLA 103
               SCOP domains d2psmc1 C:3-71 Interleukin-15 receptor subunit alpha                  SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee..........eee.ee...eee......eeeeee......eee......eee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 2psm C   3 TCPPPVSIEHADIRVKNYSVNSRERYVCNSGFKRKAGTSTLIECVINKNTNVAHWTTPSLKCIRDPSLA  71
                                    12        22        32        42        52        62         

Chain F from PDB  Type:PROTEIN  Length:68
 aligned with I15RA_MOUSE | Q60819 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:68
                                    44        54        64        74        84        94        
          I15RA_MOUSE    35 TCPPPVSIEHADIRVKNYSVNSRERYVCNSGFKRKAGTSTLIECVINKNTNVAHWTTPSLKCIRDPSL 102
               SCOP domains d2psmf_ F: Interleukin-15 receptor subunit alpha                     SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Sushi-2psmF01 F:4-64                                         ------ Pfam domains (1)
           Pfam domains (2) -Sushi-2psmF02 F:4-64                                         ------ Pfam domains (2)
         Sec.struct. author ..........ee..........eee.ee...eee......eeeeee......eee......eee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 2psm F   3 TCPPPVSIEHADIRVKNYSVNSRERYVCNSGFKRKAGTSTLIECVINKNTNVAHWTTPSLKCIRDPSL  70
                                    12        22        32        42        52        62        

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit

(-) Gene Ontology  (38, 42)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (IL15_MOUSE | P48346)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0005126    cytokine receptor binding    Interacting selectively and non-covalently with a cytokine receptor.
biological process
    GO:0001866    NK T cell proliferation    The expansion of a NK T cell population by cell division.
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0048469    cell maturation    A developmental process, independent of morphogenetic (shape) change, that is required for a cell to attain its fully functional state.
    GO:0071305    cellular response to vitamin D    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 vitamin D stimulus.
    GO:0045062    extrathymic T cell selection    The process of T cell selection that occurs in extrathymic locations, often resulting T cells of distinct specificities from those selected in the thymus.
    GO:0030212    hyaluronan metabolic process    The chemical reactions and pathways involving hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine.
    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: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:0048535    lymph node development    The process whose specific outcome is the progression of lymph nodes over time, from their formation to the mature structure. A lymph node is a round, oval, or bean shaped structure localized in clusters along the lymphatic vessels, with a distinct internal structure including specialized vasculature and B- and T-zones for the activation of lymphocytes.
    GO:0001779    natural killer cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a natural killer cell.
    GO:0048662    negative regulation of smooth muscle cell proliferation    Any process that stops, prevents or reduces the rate or extent of smooth muscle cell proliferation.
    GO:0042102    positive regulation of T cell proliferation    Any process that activates or increases the rate or extent of T cell proliferation.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0050778    positive regulation of immune response    Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0032740    positive regulation of interleukin-17 production    Any process that activates or increases the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines.
    GO:0032825    positive regulation of natural killer cell differentiation    Any process that activates or increases the frequency, rate or extent of natural killer cell differentiation.
    GO:0032819    positive regulation of natural killer cell proliferation    Any process that activates or increases the frequency, rate or extent of natural killer cell proliferation.
    GO:1904100    positive regulation of protein O-linked glycosylation    Any process that activates or increases the frequency, rate or extent of protein O-linked glycosylation.
    GO:0045580    regulation of T cell differentiation    Any process that modulates the frequency, rate or extent of T cell differentiation.
    GO:0050691    regulation of defense response to virus by host    Any host process that modulates the frequency, rate, or extent of the antiviral response of a host cell or organism.
    GO:0031667    response to nutrient levels    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
    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:0014732    skeletal muscle atrophy    A process, occurring in skeletal muscle, that is characterized by a decrease in protein content, fiber diameter, force production and fatigue resistance in response to different conditions such as starvation, aging and disuse.
cellular component
    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: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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

Chain C,F   (I15RA_MOUSE | Q60819)
biological process
    GO:0007259    JAK-STAT cascade    Any process in which STAT proteins (Signal Transducers and Activators of Transcription) and JAK (Janus Activated Kinase) proteins convey a signal to trigger a change in the activity or state of a cell. The JAK-STAT cascade begins with activation of STAT proteins by members of the JAK family of tyrosine kinases, proceeds through dimerization and subsequent nuclear translocation of STAT proteins, and ends with regulation of target gene expression by STAT proteins.
    GO:0010977    negative regulation of neuron projection development    Any process that decreases 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:0032825    positive regulation of natural killer cell differentiation    Any process that activates or increases the frequency, rate or extent of natural killer cell differentiation.
    GO:0031667    response to nutrient levels    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
cellular component
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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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