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(-) Description

Title :  SOLUTION STRUCTURE OF THE PCI DOMAIN
 
Authors :  S. Suzuki, H. Hatanaka, T. Kigawa, M. Shirouzu, Y. Hayashizaki, The Riken Genome Exploration Research Group Phase I & Ii Teams, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  02 Jun 03  (Deposition) - 29 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Helix-Turn-Helix, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Suzuki, H. Hatanaka, T. Kigawa, M. Shirouzu, Y. Hayashizaki, The Riken Genome Exploration Research Group Phase I & Ii Teams, S. Yokoyama
Solution Structure Of The Pci Domain
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COP9 COMPLEX SUBUNIT 4
    ChainsA
    EngineeredYES
    Expression System PlasmidP020826-24
    Expression System Vector TypePLASMID
    FragmentPCI DOMAIN
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    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 1UFM)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UFM)

(-) Exons   (0, 0)

(no "Exon" information available for 1UFM)

(-) 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:84
 aligned with CSN4_MOUSE | O88544 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:161
                                   245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395 
           CSN4_MOUSE   236 ASAGQQRSRMLATLFKDERCQQLAAYGILEKMYLDRIIRGNQLQEFAAMLMPHQKATTADGSSILDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVHFETREALPTWDKQIQSLCFQVNNLLEKISQTAPEWT 396
               SCOP domains d1uf                                                     ma_ A: COP9 signalosome complex subunit 4, GSN4                                                          SCOP domains
               CATH domains 1ufm                                                     A00 A:289-372 'winged helix' repressor DNA binding domain                                                CATH domains
               Pfam domains ------------------------------------------------------------PCI-1ufmA01 A:296-363                                               --------------------------------- Pfam domains
         Sec.struct. author ....-----------------------------------------------------........hhhhhhhhhhhhhhh..eeehhhhhhhh..hhhhhhhhhhhhhhh....eeee....eeee......------------------------..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ufm A 289 GSSG-----------------------------------------------------SSGGSSILDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVHFETREAS------------------------GPSSG 372
                               |     -         -         -         -         -       295       305       315       325       335       345       355       365 |       -         -      |371 
                             292                                                   293                                                                       367                      368    

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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  (1, 1)

NMR Structure

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: HTH (544)

(-) Gene Ontology  (13, 13)

NMR Structure(hide GO term definitions)
Chain A   (CSN4_MOUSE | O88544)
molecular function
    GO:0019784    NEDD8-specific protease activity    Catalysis of the hydrolysis of NEDD8, a small ubiquitin-related modifier, from previously neddylated substrates.
    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:0000338    protein deneddylation    The removal of a ubiquitin-like protein of the NEDD8 type from a protein.
cellular component
    GO:0008180    COP9 signalosome    A protein complex that catalyzes the deneddylation of proteins, including the cullin component of SCF ubiquitin E3 ligase; deneddylation increases the activity of cullin family ubiquitin ligases. The signalosome is involved in many regulatory process, including some which control development, in many species; also regulates photomorphogenesis in plants; in many species its subunits are highly similar to those of the proteasome.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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: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: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:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
    GO:0008021    synaptic vesicle    A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.

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