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(-) Description

Title :  SOLUTION STRUCTURE OF PHD DOMAIN IN DEATH INDUCER-OBLITERATOR 1(DIO-1)
 
Authors :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  25 May 04  (Deposition) - 25 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Structural Genomics, Phd Domain, Death Inducer- Obliterator 1(Dio-1), Riken Structural Genomics/Proteomics Initiative, Rsgi, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of Phd Domain In Death Inducer-Obliterator 1(Dio-1)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DEATH ASSOCIATED TRANSCRIPTION FACTOR 1
    ChainsA
    EngineeredYES
    Expression System PlasmidP030421-56
    Expression System Vector TypePLASMID
    FragmentPHD DOMAIN
    GeneRIKEN CDNA 3830408B01
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymDEATH INDUCER-OBLITERATOR-1, DIO-1

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:19 , CYS A:21 , HIS A:41 , CYS A:44BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS A:33 , CYS A:36 , CYS A:64 , CYS A:67BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_2PS50016 Zinc finger PHD-type profile.DIDO1_MOUSE265-319  1A:16-70
2ZF_PHD_1PS01359 Zinc finger PHD-type signature.DIDO1_MOUSE268-316  1A:19-67

(-) Exons   (0, 0)

(no "Exon" information available for 1WEM)

(-) Sequences/Alignments

NMR Structure
   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:76
 aligned with DIDO1_MOUSE | Q8C9B9 from UniProtKB/Swiss-Prot  Length:2256

    Alignment length:227
                                   212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       
          DIDO1_MOUSE   203 GSAEQDRPLCKQEPEASQGPVSQSETDDIENQLEGKATQGNTEENPREAGKPKPECEVYDPNALYCICRQPHNNRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILQVQDETNGSATDEQDSGCRSVGADGTDCTSIGTVEQKSGEDQGIKGRIEKAANPSGKKKLKIFQPVVEAPGAPKCIGPGCSSVAQPDSVYCSNDCILKHAAATMRFLSSG 429
               SCOP domains d1w            ema_                                    A: Death associated transcription factor 1, Datf1 (DIO-1)                                                                                                                    SCOP domains
               CATH domains 1we            mA00                                    A:1-76 Zinc/RING finger domain, C3HC4 (zinc finger)                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------PHD-1wemA01 A:18-70                                  -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...------------....-----------------------------------......................eee......eeehhhh...hhhhhhhhhh......hhhhhh.---------------------------------------------------------------------------..-----------------------------... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------ZF_PHD_2  PDB: A:16-70 UniProt: 265-319                -------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------ZF_PHD_1  PDB: A:19-67 UniProt: 268-316          ----------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wem A   1 GSS------------GSSG-----------------------------------ECEVYDPNALYCICRQPHNNRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILS---------------------------------------------------------------------------GP-----------------------------SSG  76
                              |      -     |  |-         -         -         -    |   13        23        33        43        53        63       | -         -         -         -         -         -         -         -   ||    -         -         -    |  
                              3            4  7                                   8                                                             71                                                                          72|                            74  
                                                                                                                                                                                                                             73                                

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (10, 10)

NMR Structure(hide GO term definitions)
Chain A   (DIDO1_MOUSE | Q8C9B9)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

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