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(-) Description

Title :  1.8 A CRYSTAL STRUCTURE OF MURINE GITR LIGAND DIMER EXPRESSED IN DROSOPHILA MELANOGASTER S2 CELLS
 
Authors :  K. Chattopadhyay, U. A. Ramagopal, S. G. Nathenson, S. C. Almo
Date :  20 Nov 08  (Deposition) - 30 Dec 08  (Release) - 30 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Gitrl; Glucocorticoid-Induced Tnf Receptor Ligand, Receptor, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Chattopadhyay, U. A. Ramagopal, S. G. Nathenson, S. C. Almo
1. 8 A Structure Of Murine Gitr Ligand Dimer Expressed In Drosophila Melanogaster S2 Cells.
Acta Crystallogr. , Sect. D V. 65 434 2009
PubMed-ID: 19390148  |  Reference-DOI: 10.1107/S0907444909005721
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GITR LIGAND
    Chains: A, B
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Plasmid: PMT-BIP-V5-HIS
    Expression System Strain: S2 CELLS
    Expression System Taxid: 7227
    Gene: TNFSF18, GITRL
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: GLUCOCORTICOID-INDUCED-TUMOR NECROSIS FACTOR RECEPTOR LIGAND, TUMOR NECROSIS FACTOR (LIGAND) SUPERFAMILY, MEMBER 18

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:16 , PRO A:70 , VAL A:73 , ASN A:74 , THR A:75BINDING SITE FOR RESIDUE ACT A 1

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:52 -A:72
2B:52 -B:72

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FC0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FC0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FC0)

(-) Exons   (0, 0)

(no "Exon" information available for 3FC0)

(-) 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:123
 aligned with TNF18_MOUSE | Q7TS55 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:123
                                    60        70        80        90       100       110       120       130       140       150       160       170   
          TNF18_MOUSE    51 SCMVKFELSSSKWHMTSPKPHCVNTTSDGKLKILQSGTYLIYGQVIPVDKKYIKDNAPFVVQIYKKNDVLQTLMNDFQILPIGGVYELHAGDNIYLKFNSKDHIQKTNTYWGIILMPDLPFIS 173
               SCOP domains d3fc0a_ A: Glucocorticoid-induced TNF-related ligand, TNFSF18                                                               SCOP domains
               CATH domains 3fc0A00 A:51-173  [code=2.60.120.40, no name defined]                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eeee.......eee.....eee...eeeeeeeeeee.hhhhh.....eeeeeee..eeeeeeee....eeeeeeeee....eeeeee.hhh.eeeeeeeeeeee.....eee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fc0 A  51 SCMVKFELSSSKWHMTSPKPHCVNTTSDGKLKILQSGTYLIYGQVIPVDKKYIKDNAPFVVQIYKKNDVLQTLMNDFQILPIGGVYELHAGDNIYLKFNSKDHIQKTNTYWGIILMPDLPFIS 173
                                    60        70        80        90       100       110       120       130       140       150       160       170   


Chain B from PDB  Type:PROTEIN  Length:119
 aligned with TNF18_MOUSE | Q7TS55 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:123
                                    60        70        80        90       100       110       120       130       140       150       160       170   
          TNF18_MOUSE    51 SCMVKFELSSSKWHMTSPKPHCVNTTSDGKLKILQSGTYLIYGQVIPVDKKYIKDNAPFVVQIYKKNDVLQTLMNDFQILPIGGVYELHAGDNIYLKFNSKDHIQKTNTYWGIILMPDLPFIS 173
               SCOP domains d3fc0b_ B: Glucocorticoid-induced TNF-related ligand,     TNFSF18                                                           SCOP domains
               CATH domains 3fc0B00 B:51-173  [code=2.60.120.40, no name defined]                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eeee.......eee.....eee...eeeeeeeee...hhhhh----.eeeeeee..eeeeeeee....eeeeeeeee....eeeeee.hhhhh.....eeeeee.....ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fc0 B  51 SCMVKFELSSSKWHMTSPKPHCVNTTSDGKLKILQSGTYLIYGQVIPVDKKYI----PFVVQIYKKNDVLQTLMNDFQILPIGGVYELHAGDNIYLKFNSKDHIQKTNTYWGIILMPDLPFIS 173
                                    60        70        80        90       100  |    110       120       130       140       150       160       170   
                                                                              103  108
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FC0)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TNF18_MOUSE | Q7TS55)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    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:0005164    tumor necrosis factor receptor binding    Interacting selectively and non-covalently with the tumor necrosis factor receptor.
    GO:0032813    tumor necrosis factor receptor superfamily binding    Interacting selectively and non-covalently with any member of the tumor necrosis factor receptor superfamily.
biological process
    GO:0002309    T cell proliferation involved in immune response    The expansion of a T cell population by cell division as part of an immune response.
    GO:0035741    activated CD4-positive, alpha-beta T cell proliferation    The expansion of an activated CD4-positive, alpha-beta T cell population by cell division.
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    GO:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    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:0032613    interleukin-10 production    The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0032615    interleukin-12 production    The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:2000329    negative regulation of T-helper 17 cell lineage commitment    Any process that stops, prevents or reduces the frequency, rate or extent of T-helper 17 cell lineage commitment.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:0045785    positive regulation of cell adhesion    Any process that activates or increases the frequency, rate or extent of cell adhesion.
    GO:0050729    positive regulation of inflammatory response    Any process that activates or increases the frequency, rate or extent of the inflammatory response.
    GO:0002687    positive regulation of leukocyte migration    Any process that activates or increases the frequency, rate, or extent of leukocyte migration.
    GO:0010759    positive regulation of macrophage chemotaxis    Any process that increases the rate, frequency or extent of macrophage chemotaxis. Macrophage chemotaxis is the movement of a macrophage in response to an external stimulus.
    GO:0090026    positive regulation of monocyte chemotaxis    Any process that increases the frequency, rate, or extent of monocyte chemotaxis.
    GO:0090073    positive regulation of protein homodimerization activity    Any process that increases the frequency, rate or extent of protein homodimerization, interacting selectively with an identical protein to form a homodimer.
    GO:2000348    regulation of CD40 signaling pathway    Any process that modulates the frequency, rate or extent of signaling via the CD40 signaling pathway.
    GO:0042129    regulation of T cell proliferation    Any process that modulates the frequency, rate or extent of T cell proliferation.
    GO:2000508    regulation of dendritic cell chemotaxis    Any process that modulates the frequency, rate or extent of dendritic cell chemotaxis.
    GO:0032649    regulation of interferon-gamma production    Any process that modulates the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:0032675    regulation of interleukin-6 production    Any process that modulates the frequency, rate, or extent of interleukin-6 production.
    GO:0071637    regulation of monocyte chemotactic protein-1 production    Any process that modulates the frequency, rate, or extent of production of monocyte chemotactic protein-1.
    GO:0032680    regulation of tumor necrosis factor production    Any process that modulates the frequency, rate, or extent of tumor necrosis factor production.
    GO:0033209    tumor necrosis factor-mediated signaling pathway    A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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: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
        TNF18_MOUSE | Q7TS55: 2q8o 2qdn 3b9i

(-) Related Entries Specified in the PDB File

2qdn CRYSTAL STRUCTURE OF MOUSE GITRL