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(-) Description

Title :  CRYSTAL STRUCTURE OF APO2L/TRAIL
 
Authors :  S. G. Hymowitz, M. P. O'Connell, M. H. Ultsch, A. M. De Vos, R. F. Kelley
Date :  23 Nov 99  (Deposition) - 26 Jan 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Cytokine, Tnf, Trimer, Zinc-Binding Site, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. G. Hymowitz, M. P. O'Connell, M. H. Ultsch, A. Hurst, K. Totpal, A. Ashkenazi, A. M. De Vos, R. F. Kelley
A Unique Zinc-Binding Site Revealed By A High-Resolution X-Ray Structure Of Homotrimeric Apo2L/Trail.
Biochemistry V. 39 633 2000
PubMed-ID: 10651627  |  Reference-DOI: 10.1021/BI992242L

(-) Compounds

Molecule 1 - APO2L/TNF-RELATED APOPOTIS INDUCING LIGAND (TRAIL)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorTRP PROMOTER
    FragmentTRIMERIC JELLY-ROLL DOMAIN OF APO2L
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsHUMAN PLACENTA
    TissueHUMAN PLACENTA

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2ZN1Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:230 , CL A:406BINDING SITE FOR RESIDUE ZN A 300
2AC2SOFTWARECYS A:230 , ZN A:300BINDING SITE FOR RESIDUE CL A 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DG6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DG6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DG6)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNF_2PS50049 TNF family profile.TNF10_HUMAN123-280  1A:123-280
2TNF_1PS00251 TNF family signature.TNF10_HUMAN174-190  1A:174-190
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNF_2PS50049 TNF family profile.TNF10_HUMAN123-280  3A:123-280
2TNF_1PS00251 TNF family signature.TNF10_HUMAN174-190  3A:174-190

(-) Exons   (2, 2)

Asymmetric Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002412611aENSE00001929619chr3:172241297-172241043255TNF10_HUMAN1-44440--
1.3ENST000002412613ENSE00000826259chr3:172232788-172232651138TNF10_HUMAN45-90460--
1.4aENST000002412614aENSE00001015416chr3:172229449-17222940743TNF10_HUMAN91-105150--
1.5aENST000002412615aENSE00001693878chr3:172227111-172227007105TNF10_HUMAN105-140361A:120-13011
1.7cENST000002412617cENSE00001858222chr3:172224709-1722232981412TNF10_HUMAN140-2811421A:142-281 (gaps)140

(-) 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:149
 aligned with TNF10_HUMAN | P50591 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:162
                                   129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279  
          TNF10_HUMAN   120 QRVAAHITGTRGRSNTLSSPNSKNEKALGRKINSWESSRSGHSFLSNLHLRNGELVIHEKGFYYIYSQTYFRFQEEIKENTKNDKQMVQYIYKYTSYPDPILLMKSARNSCWSKDAEYGLYSIYQGGIFELKENDRIFVSVTNEHLIDMDHEASFFGAFLVG 281
               SCOP domains d1dg6a_ A:            Apoptosis-2 ligand, apo2l/TRAIL                                                                                                              SCOP domains
               CATH domains 1dg6A00 A:1           20-281  [code=2.60.120.40, no name defined]                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee...-----------.......ee............eee.eeee..eeee...eeeeeeeeeeeeee.--........eeeeeeeee......eeeeeeeee........eeeeeeeeeeeeee....eeeeee.hhh.ee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---TNF_2  PDB: A:123-280 UniProt: 123-280                                                                                                                        - PROSITE (1)
                PROSITE (2) ------------------------------------------------------TNF_1            ------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.5a            --------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------Exon 1.7c  PDB: A:142-281 (gaps) UniProt: 140-281 [INCOMPLETE]                                                                                 Transcript 1 (2)
                 1dg6 A 120 QRVAAHITGTR-----------KNEKALGRKINSWESSRSGHSFLSNLHLRNGELVIHEKGFYYIYSQTYFRFQE--KENTKNDKQMVQYIYKYTSYPAPILLMKSARNSCWSKDAEYGLYSIYQGGIFELKENDRIFVSVTNEHLIDMDHEASFFGAFLVG 281
                                   129|        -  |    149       159       169       179       189    |  199       209       219       229       239       249       259       269       279  
                                    130         142                                                 194  |                                                                                    
                                                                                                       197                                                                                    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "Pfam Domain" information available for 1DG6)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)
Chain A   (TNF10_HUMAN | P50591)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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.
    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: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:0097296    activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway    Any process that initiates the activity of an inactive cysteine-type endopeptidase involved in the apoptotic signaling pathway.
    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:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    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:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:1902042    negative regulation of extrinsic apoptotic signaling pathway via death domain receptors    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0043280    positive regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process.
    GO:2001238    positive regulation of extrinsic apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway.
    GO:0090200    positive regulation of release of cytochrome c from mitochondria    Any process that increases the rate, frequency or extent of release of cytochrome c from mitochondria, the process in which cytochrome c is enabled to move from the mitochondrial intermembrane space into the cytosol, which is an early step in apoptosis and leads to caspase activation.
    GO:1902041    regulation of extrinsic apoptotic signaling pathway via death domain receptors    Any process that modulates the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.
    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.
cellular component
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TNF10_HUMAN | P505911d0g 1d2q 1d4v 1du3 4n90 5cir

(-) Related Entries Specified in the PDB File

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