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

(-) Description

Title :  CRYSTAL STRUCTURE OF MURINE APRIL AT PH 5.0
 
Authors :  H. J. Wallweber, D. M. Compaan, M. A. Starovasnik, S. G. Hymowitz
Date :  28 Jul 04  (Deposition) - 12 Oct 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Tnfsf, Cytokine, Jelly-Roll, Trimer, Hormone-Growth Factor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Wallweber, D. M. Compaan, M. A. Starovasnik, S. G. Hymowitz
The Crystal Structure Of A Proliferation-Inducing Ligand, April.
J. Mol. Biol. V. 343 283 2004
PubMed-ID: 15451660  |  Reference-DOI: 10.1016/J.JMB.2004.08.040

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-32A (MODIFIED)
    Expression System Strain: ORIGAMI (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: TNF DOMAIN OF MURINE APRIL
    Gene: TNFSF13, APRIL
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: A PROLIFERATION- INDUCING LIGAND, APRIL

 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 1U5X)

(-) Sites  (0, 0)

(no "Site" information available for 1U5X)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:187 -A:202

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U5X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U5X)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNF_2PS50049 TNF family profile.TNF13_MOUSE108-241  1A:108-241
2TNF_1PS00251 TNF family signature.TNF13_MOUSE146-162  1A:146-162
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNF_2PS50049 TNF family profile.TNF13_MOUSE108-241  3A:108-241
2TNF_1PS00251 TNF family signature.TNF13_MOUSE146-162  3A:146-162

(-) Exons   (0, 0)

(no "Exon" information available for 1U5X)

(-) 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:130
 aligned with TNF13_MOUSE | Q9D777 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:137
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       
          TNF13_MOUSE   105 KHSVLHLVPVNITSKADSDVTEVMWQPVLRRGRGLEAQGDIVRVWDTGIYLLYSQVLFHDVTFTMGQVVSREGQGRRETLFRCIRSMPSDPDRAYNSCYSAGVFHLHQGDIITVKIPRANAKLSLSPHGTFLGFVKL 241
               SCOP domains d1u5xa_ A: A p    roliferation-inducing ligand, APRIL                                                                                     SCOP domains
               CATH domains 1u5xA00 A:105-    241  [code=2.60.120.40, no name defined]                                                                                CATH domains
               Pfam domains --------------    ------TNF-1u5xA01 A:129-241                                                                                             Pfam domains
         Sec.struct. author ...eeeeeeeeee.----..eeeeeeeeeee...eeee..eeee...eeeeeeeeeee.........eeeee....eeeeee........---..eeeeeeeeeee....eeeeee..............eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---TNF_2  PDB: A:108-241 UniProt: 108-241                                                                                                 PROSITE (1)
                PROSITE (2) -----------------------------------------TNF_1            ------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u5x A 105 KHSVLHLVPVNITS----DVTEVMWQPVLRRGRGLEAQGDIVRVWDTGIYLLYSQVLFHDVTFTMGQVVSREGQGRRETLFRCIRSMPSD---AYNSCYSAGVFHLHQGDIITVKIPRANAKLSLSPHGTFLGFVKL 241
                                   114   |   124       134       144       154       164       174       184       194   |   204       214       224       234       
                                       118  123                                                                    194 198
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: C1q_TNF (45)
(-)
Family: TNF (37)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A   (TNF13_MOUSE | Q9D777)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0005164    tumor necrosis factor receptor binding    Interacting selectively and non-covalently with the tumor necrosis factor receptor.
biological process
    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:0016064    immunoglobulin mediated immune response    An immune response mediated by immunoglobulins, whether cell-bound or in solution.
    GO:0002426    immunoglobulin production in mucosal tissue    The synthesis and release of immunoglobulin in the mucosal tissue.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0002636    positive regulation of germinal center formation    Any process that activates or increases the frequency, rate, or extent of germinal center formation.
    GO:0048298    positive regulation of isotype switching to IgA isotypes    Any process that activates or increases the frequency, rate or extent of isotype switching to IgA isotypes.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 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 1u5x)
 
  Sites
(no "Sites" information available for 1u5x)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1u5x)
 
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
[ Asym. Unit PNG format | Biol. Unit 1 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1u5x
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TNF13_MOUSE | Q9D777
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  TNF13_MOUSE | Q9D777
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TNF13_MOUSE | Q9D777: 1u5y 1u5z 1xu1 1xu2 3k48

(-) Related Entries Specified in the PDB File

1u5y SAME PROTEIN CRYSTALLZED IN C2 SPACE GROUP AT PH 8.0
1u5z SAME PROTEIN CRYSTALLZED IN I23 SPACE GROUP AT PH 8.5