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(-) Description

Title :  THE STRUCTURE OF TL1A-DCR3 COMPLEX
 
Authors :  C. Zhan, Y. Patskovsky, Q. Yan, Z. Li, U. A. Ramagopal, S. G. Nathenson, S
Date :  09 Apr 10  (Deposition) - 23 Feb 11  (Release) - 23 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A,D
Biol. Unit 1:  A,D  (3x)
Keywords :  Dcr3, Tl1A, Tnf, Tnfr, Decoy Receptor, Immunity, Disulfide Bond, Glycoprotein, Secreted, Receptor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Zhan, Y. Patskovsky, Q. Yan, Z. Li, U. Ramagopal, H. Cheng, M. Brenowitz, X. Hui, S. G. Nathenson, S. C. Almo
Decoy Strategies: The Structure Of Tl1A:Dcr3 Complex.
Structure V. 19 162 2011
PubMed-ID: 21300286  |  Reference-DOI: 10.1016/J.STR.2010.12.004

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 15, SECRETED FORM
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21-AI
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 72-251
    GeneTL1, TNFSF15, VEGI
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymVASCULAR ENDOTHELIAL CELL GROWTH INHIBITOR, TNF LIGAND- RELATED MOLECULE 1, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 15, MEMBRANE FORM, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 15, SECRETED FORM
 
Molecule 2 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 6B
    ChainsD
    EngineeredYES
    Expression SystemDROSOPHILA
    Expression System Cell LineS2
    Expression System PlasmidPMT/BIP/V5-HIS
    Expression System Taxid7215
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 30-195
    GeneDCR3, TNFRSF6B
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDECOY RECEPTOR FOR FAS LIGAND, DECOY RECEPTOR 3, DCR3, M68

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AD
Biological Unit 1 (3x)AD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3MI8)

(-) Sites  (0, 0)

(no "Site" information available for 3MI8)

(-) SS Bonds  (7, 7)

Asymmetric Unit
No.Residues
1D:49 -D:62
2D:52 -D:70
3D:73 -D:88
4D:91 -D:105
5D:95 -D:113
6D:115 -D:126
7D:132 -D:150

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MI8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_043130F110LTNF15_HUMANPolymorphism16931745AF43L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_043130F110LTNF15_HUMANPolymorphism16931745AF43L

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

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNFR_NGFR_1PS00652 TNFR/NGFR family cysteine-rich region signature.TNF6B_HUMAN70-113  1D:70-113
2TNFR_NGFR_2PS50050 TNFR/NGFR family cysteine-rich region domain profile.TNF6B_HUMAN72-113
152-193
  1D:72-113
-
3TNF_2PS50049 TNF family profile.TNF15_HUMAN97-251  1A:30-184
Biological Unit 1 (3, 9)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNFR_NGFR_1PS00652 TNFR/NGFR family cysteine-rich region signature.TNF6B_HUMAN70-113  3D:70-113
2TNFR_NGFR_2PS50050 TNFR/NGFR family cysteine-rich region domain profile.TNF6B_HUMAN72-113
152-193
  3D:72-113
-
3TNF_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:26-349
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:144
 aligned with TNF15_HUMAN | O95150 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:159
                                   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242         
          TNF15_HUMAN    93 DKPRAHLTVVRQTPTQHFKNQFPALHWEHELGLAFTKNRMNYTNKFLLIPESGDYFIYSQVTFRGMTSECSEIRQAGRPNKPDSITVVITKVTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMFSLQEGDKLMVNVSDISLVDYTKEDKTFFGAFLL 251
               SCOP domains d3mi8a_ A: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------TNF-3mi8A01 A:50-184                                                                                                                    Pfam domains
         Sec.struct. author ...eeeeee.................ee......eee...eee..eee....eeeeeeeeeeeee.---------------..eeeeeeeee.......eeeeeeeee.......eeeeeeeeeeeee....eeeeee.hhhhh........eeeeee. Sec.struct. author
                 SAPs(SNPs) -----------------L--------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ----TNF_2  PDB: A:30-184 UniProt: 97-251                                                                                                                        PROSITE (3)
           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)
                 3mi8 A  26 DKPRAHLTVVRQTPTQHFKNQFPALHWEHELGLAFTKNRMNYTNKFLLIPESGDYFIYSQVTFRGM---------------PDSITVVITKVTDSYPEPTQLLMGTKSVSEVGSNWFQPIYLGAMFSLQEGDKLMVNVSDISLVDYTKEDKTFFGAFLL 184
                                    35        45        55        65        75        85     |   -         - |     115       125       135       145       155       165       175         
                                                                                            91             107                                                                             

Chain D from PDB  Type:PROTEIN  Length:109
 aligned with TNF6B_HUMAN | O95407 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:118
                                    42        52        62        72        82        92       102       112       122       132       142        
          TNF6B_HUMAN    33 TPTYPWRDAETGERLVCAQCPPGTFVQRPCRRDSPTTCGPCPPRHYTQFWNYLERCRYCNVLCGEREEEARACHATHNRACRCRTGFFAHAGFCLEHASCPPGAGVIAPGTPSQNTQC 150
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------TNFR_c6-3mi8D01 D:73-113                 ------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......eeeee.....eeeee........eeee....ee..........ee........eeeee........eeee...eeee..eeee....---------......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------TNFR_NGFR_1  PDB: D:70-113 UniProt: 70-113  ------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------TNFR_NGFR_2  PDB: D:72-113 UniProt: 72-113------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3mi8 D  33 TPTYPWRDAETGERLVCAQCPPGTFVQRPCRRDSPTTCGPCPPRHYTQFWNYLERCRYCNVLCGEREEEARACHATHNRACRCRTGFFAHAGFCLEHASC---------GTPSQNTQC 150
                                    42        52        62        72        82        92       102       112       122       132       142        
                                                                                                                             132       142        

   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 3MI8)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: C1q_TNF (45)

(-) Gene Ontology  (27, 32)

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.

Chain D   (TNF6B_HUMAN | O95407)
molecular function
    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:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0005031    tumor necrosis factor-activated receptor activity    Combining with tumor necrosis factor, a proinflammatory cytokine produced by monocytes and macrophages, to initiate a change in cell function.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0097190    apoptotic signaling pathway    A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
    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:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    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:0043410    positive regulation of MAPK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TNF15_HUMAN | O951502o0o 2qe3 2re9 2rjk 2rjl 3k51
        TNF6B_HUMAN | O954073k51 3mhd 4j6g 4kgg 4kgq 4msv 5l36

(-) Related Entries Specified in the PDB File

2qe3 TL1A STRUCTURE
3k51 TL1A-DCR3 STRCUTRE
3mhd DCR3 STRUCTURE