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(-) Description

Title :  CRYSTAL STRUCTURE OF TL1A
 
Authors :  T. C. Jin, S. Kim, F. Guo, A. J. Howard, Y. Z. Zhang
Date :  27 Nov 06  (Deposition) - 30 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Vegi, Homotrimer, Metal Binding, Cancer, Angiogenesis, Inflammation, Cytokine, Hormone-Growth Factor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Jin, F. Guo, S. Kim, A. Howard, Y. Z. Zhang
X-Ray Crystal Structure Of Tnf Ligand Family Member Tl1A At 2. 1A.
Biochem. Biophys. Res. Commun. V. 364 1 2007
PubMed-ID: 17935696  |  Reference-DOI: 10.1016/J.BBRC.2007.09.097

(-) Compounds

Molecule 1 - TNF SUPERFAMILY LIGAND TL1A
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPRSFDUET-1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneTNFSF15
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 15

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:120BINDING SITE FOR RESIDUE MG A 271

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O0O)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg B:170 -Pro B:171

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 3)

Asymmetric/Biological Unit (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_043130F110LTNF15_HUMANPolymorphism16931745A/B/CF110L

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

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNF_2PS50049 TNF family profile.TNF15_HUMAN97-251
 
 
  3A:97-251
B:97-251
C:97-251

(-) Exons   (2, 6)

Asymmetric/Biological Unit (2, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003740451ENSE00001462247chr9:117568406-117568083324TNF15_HUMAN1-70700--
1.2ENST000003740452ENSE00001212373chr9:117555848-11755580643TNF15_HUMAN71-85150--
1.3bENST000003740453bENSE00001212368chr9:117554734-11755468748TNF15_HUMAN85-101173A:92-101
B:92-101
C:92-101
10
10
10
1.4cENST000003740454cENSE00001925927chr9:117553186-1175516001587TNF15_HUMAN101-2511513A:101-251 (gaps)
B:101-251 (gaps)
C:101-251 (gaps)
151
151
151

(-) 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:153
 aligned with TNF15_HUMAN | O95150 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:160
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
          TNF15_HUMAN    92 GDKPRAHLTVVRQTPTQHFKNQFPALHWEHELGLAFTKNRMNYTNKFLLIPESGDYFIYSQVTFRGMTSECSEIRQAGRPNKPDSITVVITKVTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMFSLQEGDKLMVNVSDISLVDYTKEDKTFFGAFLL 251
               SCOP domains d2o0oa_ A: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..........................eee...eee..eee....eeeeeeeeeeeeee....-------.....eeeeeeeeee............eeeee.....eeeeeeeeeeeeee....eeeeee.hhhhh........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------L--------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----TNF_2  PDB: A:97-251 UniProt: 97-251                                                                                                                        PROSITE
           Transcript 1 (1) Exon 1.3b ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.4c  PDB: A:101-251 (gaps) UniProt: 101-251                                                                                                       Transcript 1 (2)
                 2o0o A  92 GDKPRAHLTVVRQTPTQHFKNQFPALHWEHELGLAFTKNRMNYTNKFLLIPESGDYFIYSQVTFRGMTSEC-------RPNKPDSITVVITKVTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMFSLQEGDKLMVNVSDISLVDYTKEDKTFFGAFLL 251
                                   101       111       121       131       141       151       161|      171       181       191       201       211       221       231       241       251
                                                                                                162     170                                                                                 

Chain B from PDB  Type:PROTEIN  Length:153
 aligned with TNF15_HUMAN | O95150 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:160
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
          TNF15_HUMAN    92 GDKPRAHLTVVRQTPTQHFKNQFPALHWEHELGLAFTKNRMNYTNKFLLIPESGDYFIYSQVTFRGMTSECSEIRQAGRPNKPDSITVVITKVTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMFSLQEGDKLMVNVSDISLVDYTKEDKTFFGAFLL 251
               SCOP domains d2o0ob_ B: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..........................eee...eee..eee....eeeeeeeeeeeeee....-------.....eeeeeeeeee.......eeeeeeeeee.....eeeeeeeeeeeeee....eeeeee.hhhhh........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------L--------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----TNF_2  PDB: B:97-251 UniProt: 97-251                                                                                                                        PROSITE
           Transcript 1 (1) Exon 1.3b ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.4c  PDB: B:101-251 (gaps) UniProt: 101-251                                                                                                       Transcript 1 (2)
                 2o0o B  92 GDKPRAHLTVVRQTPTQHFKNQFPALHWEHELGLAFTKNRMNYTNKFLLIPESGDYFIYSQVTFRGMTSEC-------RPNKPDSITVVITKVTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMFSLQEGDKLMVNVSDISLVDYTKEDKTFFGAFLL 251
                                   101       111       121       131       141       151       161|      171       181       191       201       211       221       231       241       251
                                                                                                162     170                                                                                 

Chain C from PDB  Type:PROTEIN  Length:152
 aligned with TNF15_HUMAN | O95150 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:160
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
          TNF15_HUMAN    92 GDKPRAHLTVVRQTPTQHFKNQFPALHWEHELGLAFTKNRMNYTNKFLLIPESGDYFIYSQVTFRGMTSECSEIRQAGRPNKPDSITVVITKVTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMFSLQEGDKLMVNVSDISLVDYTKEDKTFFGAFLL 251
               SCOP domains d2o0oc_ C: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------TNF-2o0oC01 C:117-251                                                                                                                   Pfam domains (1)
           Pfam domains (2) -------------------------TNF-2o0oC02 C:117-251                                                                                                                   Pfam domains (2)
           Pfam domains (3) -------------------------TNF-2o0oC03 C:117-251                                                                                                                   Pfam domains (3)
         Sec.struct. author ....eeeeee.................ee......eee.........ee....eeeeeeeeeeeeee....--------....eeeeeeeeee.......eeeeeeeeee.....eeeeeeeeeeeeee....eeeeee.hhhhh........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------L--------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----TNF_2  PDB: C:97-251 UniProt: 97-251                                                                                                                        PROSITE
           Transcript 1 (1) Exon 1.3b ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.4c  PDB: C:101-251 (gaps) UniProt: 101-251                                                                                                       Transcript 1 (2)
                 2o0o C  92 GDKPRAHLTVVRQTPTQHFKNQFPALHWEHELGLAFTKNRMNYTNKFLLIPESGDYFIYSQVTFRGMTSEC--------PNKPDSITVVITKVTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMFSLQEGDKLMVNVSDISLVDYTKEDKTFFGAFLL 251
                                   101       111       121       131       141       151       161|      171       181       191       201       211       221       231       241       251
                                                                                                162      171                                                                                

   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, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2O0O)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: C1q_TNF (45)
(-)
Family: TNF (37)
1aTNF-2o0oC01C:117-251
1bTNF-2o0oC02C:117-251
1cTNF-2o0oC03C:117-251

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (TNF15_HUMAN | O95150)
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:0005164    tumor necrosis factor receptor binding    Interacting selectively and non-covalently with the tumor necrosis factor receptor.
biological process
    GO:0007250    activation of NF-kappaB-inducing kinase activity    The stimulation of the activity of NF-kappaB-inducing kinase through phosphorylation at specific residues.
    GO:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0042107    cytokine metabolic process    The chemical reactions and pathways involving cytokines, any of a group of proteins or glycoproteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity.
    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: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: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: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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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
        TNF15_HUMAN | O951502qe3 2re9 2rjk 2rjl 3k51 3mi8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2O0O)