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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN TL1A EXTRACELLULAR DOMAIN
 
Authors :  C. Zhan, Q. Yan, Y. Patskovsky, W. Shi, R. Toro, J. Bonanno, S. G. Nathens S. C. Almo
Date :  22 Jun 07  (Deposition) - 17 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Tl1A, Tnfsf, Cytokine; , Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Zhan, Q. Yan, Y. Patskovsky, Z. Li, R. Toro, A. Meyer, H. Cheng, M. Brenowitz, S. G. Nathenson, S. C. Almo
Biochemical And Structural Characterization Of The Human Tl1A Ectodomain.
Biochemistry V. 48 7636 2009
PubMed-ID: 19522538  |  Reference-DOI: 10.1021/BI900031W

(-) Compounds

Molecule 1 - TNF SUPERFAMILY LIGAND TL1A
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-28A
    Expression System StrainBL21-AI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentEXTRACELLULAR DOMAIN, RESIDUES 72-251
    GeneTNFSF15
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTUMOR NECROSIS FACTOR LIGAND, SUPERFAMILY, MEMBER 15

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:132 , GLN A:143BINDING SITE FOR RESIDUE CL A 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QE3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:25 -Asp A:26
2Gly A:138 -Ser A:139

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QE3)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNF_2PS50049 TNF family profile.TNF15_HUMAN97-251  1A:30-184
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNF_2PS50049 TNF family profile.TNF15_HUMAN97-251  3A:30-184

(-) Exons   (2, 2)

Asymmetric Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003740451ENSE00001462247chr9:117568406-117568083324TNF15_HUMAN1-70700--
1.2ENST000003740452ENSE00001212373chr9:117555848-11755580643TNF15_HUMAN71-85150--
1.3bENST000003740453bENSE00001212368chr9:117554734-11755468748TNF15_HUMAN85-101171A:23-3412
1.4cENST000003740454cENSE00001925927chr9:117553186-1175516001587TNF15_HUMAN101-2511511A:34-184 (gaps)151

(-) 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:140
 aligned with TNF15_HUMAN | O95150 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:162
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249  
          TNF15_HUMAN    90 ADGDKPRAHLTVVRQTPTQHFKNQFPALHWEHELGLAFTKNRMNYTNKFLLIPESGDYFIYSQVTFRGMTSECSEIRQAGRPNKPDSITVVITKVTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMFSLQEGDKLMVNVSDISLVDYTKEDKTFFGAFLL 251
               SCOP domains d2qe3a_ A: automa       ted matches                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------------       ---TNF-2qe3A01 A:50-184                                                                                                                    Pfam domains
         Sec.struct. author ......eeeeee.....-------.....ee......eee...eee..eee....eeeeeeeeeeee.---------------...eeeeeeeee.......eeeeeeeee........eeeeeeeeeeee....eeeeee.hhhhh........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------TNF_2  PDB: A:30-184 UniProt: 97-251                                                                                                                        PROSITE
           Transcript 1 (1) Exon 1.3b   ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.4c  PDB: A:34-184 (gaps) UniProt: 101-251                                                                                                        Transcript 1 (2)
                 2qe3 A  23 ADGDKPRAHLTVVRQTP-------FPALHWEHELGLAFTKNRMNYTNKFLLIPESGDYFIYSQVTFRG---------------KPDSITVVITKVTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMFSLQEGDKLMVNVSDISLVDYTKEDKTFFGAFLL 184
                                    32      |  -    |   52        62        72        82       | -         -   |   112       122       132       142       152       162       172       182  
                                           39      47                                         90             106                                                                              

   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  (0, 0)

(no "CATH Domain" information available for 2QE3)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: C1q_TNF (45)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A   (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 | O951502o0o 2re9 2rjk 2rjl 3k51 3mi8

(-) Related Entries Specified in the PDB File

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