Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN GITRL
 
Authors :  K. Chattopadhyay, U. A. Ramagopal, S. G. Nathenson, S. C. Almo
Date :  24 May 07  (Deposition) - 13 Nov 07  (Release) - 30 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Gitrl; Glucocorticoid-Induced Tnf Receptor Ligand, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Chattopadhyay, U. A. Ramagopal, A. Mukhopadhaya, V. N. Malashkevich, T. P. Dilorenzo, M. Brenowitz, S. G. Nathenson, S. C. Almo
Assembly And Structural Properties Of Glucocorticoid-Induced Tnf Receptor Ligand: Implications For Function.
Proc. Natl. Acad. Sci. Usa V. 104 19452 2007
PubMed-ID: 18040044  |  Reference-DOI: 10.1073/PNAS.0709264104
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 18
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-14B
    Expression System StrainROSETTA (DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentEXTRACELLULAR, TNF HOMOLOGY DOMAIN
    GeneTNFSF18, AITRL, GITRL, TL6
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGLUCOCORTICOID-INDUCED TNF-RELATED LIGAND, HGITRL, ACTIVATION-INDUCIBLE TNF-RELATED LIGAND, AITRL

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2Q1M)

(-) Sites  (0, 0)

(no "Site" information available for 2Q1M)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:58 -A:78

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:63 -Pro A:64
2Leu A:65 -Pro A:66
3Glu A:75 -Pro A:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q1M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q1M)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q1M)

(-) 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:116
 aligned with TNF18_HUMAN | Q9UNG2 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:116
                                    88        98       108       118       128       138       148       158       168       178       188      
          TNF18_HUMAN    79 PCMAKFGPLPSKWQMASSEPPCVNKVSDWKLEILQNGLYLIYGQVAPNANYNDVAPFEVRLYKNKDMIQTLTNKSKIQNVGGTYELHVGDTIDLIFNSEHQVLKNNTYWGIILLAN 194
               SCOP domains d2q1ma1 A:57-172 Glucocorticoid-induced TNF-related ligand, TNFSF18                                                  SCOP domains
               CATH domains 2q1mA00 A:57-172  [code=2.60.120.40, no name defined]                                                                CATH domains
               Pfam domains ----------TNF-2q1mA01 A:67-155                                                                     ----------------- Pfam domains
         Sec.struct. author ..eeee......eeee......eeeee..eeee...eeeeeeeee.............eeeee..eeeeee......ee..eeeee....eeeeee...........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2q1m A  57 PCMAKFGPLPSKWQMASSEPPCVNKVSDWKLEILQNGLYLIYGQVAPNANYNDVAPFEVRLYKNKDMIQTLTNKSKIQNVGGTYELHVGDTIDLIFNSEHQVLKNNTYWGIILLAN 172
                                    66        76        86        96       106       116       126       136       146       156       166      

   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, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: C1q_TNF (45)

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A   (TNF18_HUMAN | Q9UNG2)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    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: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: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: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: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:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    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: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: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: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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2q1m)
 
  Sites
(no "Sites" information available for 2q1m)
 
  Cis Peptide Bonds
    Glu A:75 - Pro A:76   [ RasMol ]  
    Gly A:63 - Pro A:64   [ RasMol ]  
    Leu A:65 - Pro A:66   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2q1m
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TNF18_HUMAN | Q9UNG2
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  TNF18_HUMAN | Q9UNG2
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TNF18_HUMAN | Q9UNG22r30 2r32 3b93 3b94

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2Q1M)