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(-) Description

Title :  THE S-SAD PHASED CRYSTAL STRUCTURE OF THE ECTO-DOMAIN OF DEATH RECEPTOR 6 (DR6)
 
Authors :  H. Ru, L. X. Zhao, W. Ding, L. Y. Jiao, N. Shaw, L. G. Zhang, L. W. Hung, N. Ma S. Wakatsuki, Z. J. Liu
Date :  06 Oct 11  (Deposition) - 02 May 12  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Trigger Apoptosis, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Ru, L. Zhao, W. Ding, L. Jiao, N. Shaw, W. Liang, L. Zhang, L. W. Hung, N. Matsugaki, S. Wakatsuki, Z. J. Liu
S-Sad Phasing Study Of Death Receptor 6 And Its Solution Conformation Revealed By Saxs
Acta Crystallogr. , Sect. D V. 68 521 2012
PubMed-ID: 22525750  |  Reference-DOI: 10.1107/S0907444912004490

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 21
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCYSTEINE RICH DOMAIN
    GeneTNFRSF21, DR6, UNQ437/PRO868
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDEATH RECEPTOR 6

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3U3P)

(-) Sites  (0, 0)

(no "Site" information available for 3U3P)

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:67 -A:80
2A:70 -A:88
3A:91 -A:106
4A:109 -A:123
5A:113 -A:131
6A:133 -A:144
7A:150 -A:168
8A:171 -A:186
9A:192 -A:211

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Trp A:115 -Pro A:116

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U3P)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNFR_NGFR_2PS50050 TNFR/NGFR family cysteine-rich region domain profile.TNR21_HUMAN90-131  1A:90-131
2TNFR_NGFR_1PS00652 TNFR/NGFR family cysteine-rich region signature.TNR21_HUMAN91-133  1A:91-133
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNFR_NGFR_2PS50050 TNFR/NGFR family cysteine-rich region domain profile.TNR21_HUMAN90-131  2A:90-131
2TNFR_NGFR_1PS00652 TNFR/NGFR family cysteine-rich region signature.TNR21_HUMAN91-133  2A:91-133

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002968611ENSE00001226615chr6:47277641-47277152490TNR21_HUMAN1-32320--
1.2ENST000002968612ENSE00000973751chr6:47254331-47253680652TNR21_HUMAN33-2502181A:51-214164
1.3aENST000002968613aENSE00001139134chr6:47252168-47251674495TNR21_HUMAN250-4151660--
1.4ENST000002968614ENSE00001139126chr6:47221257-47220992266TNR21_HUMAN415-503890--
1.5ENST000002968615ENSE00000973756chr6:47202634-47202406229TNR21_HUMAN504-580770--
1.6bENST000002968616bENSE00001084008chr6:47200730-471992681463TNR21_HUMAN580-655760--

(-) 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:164
 aligned with TNR21_HUMAN | O75509 from UniProtKB/Swiss-Prot  Length:655

    Alignment length:164
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    
          TNR21_HUMAN    51 IGTYRHVDRATGQVLTCDKCPAGTYVSEHCTNTSLRVCSSCPVGTFTRHENGIEKCHDCSQPCPWPMIEKLPCAALTDRECTCPPGMFQSNATCAPHTVCPVGWGVRKKGTETEDVRCKQCARGTFSDVPSSVMKCKAYTDCLSQNLVVIKPGTKETDNVCGTL 214
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......eeeee.....eeeee........eeee....ee..........ee.........eeee........eee....eeee..eeee.......eeeee........eeee....ee..........ee...hhhhh.eeee........eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------TNFR_NGFR_2  PDB: A:90-131 UniProt: 90-131----------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------TNFR_NGFR_1  PDB: A:91-133 UniProt: 91-133 --------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.2  PDB: A:51-214 UniProt: 33-250 [INCOMPLETE]                                                                                                                 Transcript 1
                 3u3p A  51 IGTYRHVDRATGQVLTCDKCPAGTYVSEHCTNTSLRVCSSCPVGTFTRHENGIEKCHDCSQPCPWPMIEKLPCAALTDRECTCPPGMFQSNATCAPHTVCPVGWGVRKKGTETEDVRCKQCARGTFSDVPSSVMKCKAYTDCLSQNLVVIKPGTKETDNVCGTL 214
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    

   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  (0, 0)

(no "SCOP Domain" information available for 3U3P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3U3P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U3P)

(-) Gene Ontology  (33, 33)

Asymmetric Unit(hide GO term definitions)
Chain A   (TNR21_HUMAN | O75509)
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: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:0001783    B cell apoptotic process    Any apoptotic process in a B cell, a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    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:0071356    cellular response to tumor necrosis factor    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
    GO:0006959    humoral immune response    An immune response mediated through a body fluid.
    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: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:0042552    myelination    The process in which myelin sheaths are formed and maintained around neurons. Oligodendrocytes in the brain and spinal cord and Schwann cells in the peripheral nervous system wrap axons with compact layers of their plasma membrane. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier.
    GO:0030889    negative regulation of B cell proliferation    Any process that stops, prevents or reduces the rate or extent of B cell proliferation.
    GO:0042130    negative regulation of T cell proliferation    Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
    GO:2001180    negative regulation of interleukin-10 secretion    Any process that stops, prevents or reduces the frequency, rate or extent of interleukin-10 secretion.
    GO:2000666    negative regulation of interleukin-13 secretion    Any process that stops, prevents or reduces the frequency, rate or extent of interleukin-13 secretion.
    GO:2000663    negative regulation of interleukin-5 secretion    Any process that stops, prevents or reduces the frequency, rate or extent of interleukin-5 secretion.
    GO:0031642    negative regulation of myelination    Any process that stops, prevents, or reduces the frequency, rate or extent of the formation of a myelin sheath around nerve axons.
    GO:0051402    neuron apoptotic process    Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
    GO:0097252    oligodendrocyte apoptotic process    Any apoptotic process in an oligodendrocyte. Oligodendrocytes belong to a class of large neuroglial (macroglial) cells in the central nervous system, where they form the insulating myelin sheath of axons.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0048713    regulation of oligodendrocyte differentiation    Any process that modulates the frequency, rate or extent of oligodendrocyte differentiation.
    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: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:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    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:0031226    intrinsic component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane.
    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
        TNR21_HUMAN | O755092dbh 3qo4 3u3q 3u3s 3u3t 3u3v

(-) Related Entries Specified in the PDB File

3u3q 3u3s 3u3t 3u3v