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(-) Description

Title :  SOLUTION STRUCTURE OF THE MA3 DOMAIN OF HUMAN PROGRAMMED CELL DEATH 4
 
Authors :  T. Nagata, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  24 Mar 06  (Deposition) - 24 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Ma3, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Nagata, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Solution Structure Of The Ma3 Domain Of Human Programmed Cell Death 4
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROGRAMMED CELL DEATH 4, ISOFORM 1
    ChainsA
    EngineeredYES
    Expression System PlasmidP050302-19
    Expression System Vector TypePLASMID
    FragmentMA3
    GenePDCD4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2GGF)

(-) Sites  (0, 0)

(no "Site" information available for 2GGF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2GGF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MIPS51366 MI domain profile.PDCD4_HUMAN163-284
326-449
  1-
A:327-449

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002801541aENSE00001922986chr10:112631565-112631776212PDCD4_HUMAN-00--
1.2ENST000002801542ENSE00002190882chr10:112635724-112635828105PDCD4_HUMAN1-15150--
1.6aENST000002801546aENSE00001380538chr10:112640991-112641293303PDCD4_HUMAN15-1161020--
1.7ENST000002801547ENSE00000995567chr10:112642761-11264285595PDCD4_HUMAN116-147320--
1.8cENST000002801548cENSE00001094657chr10:112645011-112645124114PDCD4_HUMAN148-185380--
1.9eENST000002801549eENSE00002200197chr10:112647423-112647644222PDCD4_HUMAN186-259740--
1.10ENST0000028015410ENSE00001788034chr10:112649291-11264938898PDCD4_HUMAN260-292330--
1.11aENST0000028015411aENSE00001772839chr10:112650314-112650428115PDCD4_HUMAN292-330391A:320-330 (gaps)15
1.12bENST0000028015412bENSE00001599108chr10:112653849-112653956108PDCD4_HUMAN331-366361A:331-36636
1.13ENST0000028015413ENSE00001674744chr10:112654170-112654280111PDCD4_HUMAN367-403371A:367-40337
1.14bENST0000028015414bENSE00001636249chr10:112655706-112655845140PDCD4_HUMAN404-450471A:404-45047
1.15eENST0000028015415eENSE00001840051chr10:112657786-1126597641979PDCD4_HUMAN450-469201A:450-456 (gaps)10

(-) 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:137
 aligned with PDCD4_HUMAN | Q53EL6 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:144
                                   325       335       345       355       365       375       385       395       405       415       425       435       445       455    
          PDCD4_HUMAN   316 GSGGGQQSVNHLVKEIDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIIMVLESTGESTFKMILDLLKSLWKSSTITVDQMKRGYERIYNEIPDINLDVPHSYSVLERFVEECFQAGIISKQLRDLCPSRGRKRFVSEG 459
               SCOP domains d2ggf    a_ A: automated matches                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....----...hhhhhhhhhhhhhh..hhhhhhhhhh......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhh....hhhhhh.......---... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------MI  PDB: A:327-449 UniProt: 326-449                                                                                         ---------- PROSITE
           Transcript 1 (1) Exon 1.11a     Exon 1.12b  PDB: A:331-366          Exon 1.13  PDB: A:367-403            Exon 1.14b  PDB: A:404-450 UniProt: 404-450    --------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------------Exon 1.15e Transcript 1 (2)
                 2ggf A 320 GSSGS----SGLVKEIDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIIMVLESTGESTFKMILDLLKSLWKSSTITVDQMKRGYERIYNEIPDINLDVPHSYSVLERFVEECFQAGIISKQLRDLCPSRSGP---SSG 456
                                |  325       335       345       355       365       375       385       395       405       415       425       435       445       | - |  
                              324  325                                                                                                                             453 454  

   Legend:   → Mismatch (orange background)
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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)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GGF)

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A   (PDCD4_HUMAN | Q53EL6)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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).
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:0007569    cell aging    An aging process that has as participant a cell after a cell has stopped dividing. Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469).
    GO:0043508    negative regulation of JUN kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of JUN kinase activity.
    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:0045786    negative regulation of cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
    GO:1904761    negative regulation of myofibroblast differentiation    Any process that stops, prevents or reduces the frequency, rate or extent of myofibroblast differentiation.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0034393    positive regulation of smooth muscle cell apoptotic process    Any process that activates or increases the frequency, rate, or extent of smooth muscle cell apoptotic process.
    GO:0051246    regulation of protein metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PDCD4_HUMAN | Q53EL62kzt 2rg8 2zu6 3eij

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