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(-) Description

Title :  NEDD8 SOLUTION STRUCTURE
 
Authors :  Y. S. Choi, Y. H. Jeon, C. Cheong
Date :  09 Sep 09  (Deposition) - 03 Nov 09  (Release) - 03 Nov 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nedd8, Isopeptide Bond, Nucleus, Ubl Conjugation Pathway, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. S. Choi, Y. H. Jeon, K. S. Ryu, C. Cheong
60Th Residues Of Ubiquitin And Nedd8 Are Located Out Of E2-Binding Surfaces, But Are Important For K48 Ubiquitin-Linkage.
Febs Lett. V. 583 3323 2009
PubMed-ID: 19782077  |  Reference-DOI: 10.1016/J.FEBSLET.2009.09.034
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEDD8
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET21A
    Expression System Vector TypeVECTOR
    GeneNEDD8
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBIQUITIN-LIKE PROTEIN NEDD8, NEDDYLIN, NEURAL PRECURSOR CELL EXPRESSED DEVELOPMENTALLY DOWN-REGULATED PROTEIN 8, NEDD-8

 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 2KO3)

(-) Sites  (0, 0)

(no "Site" information available for 2KO3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2KO3)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KO3)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.NEDD8_HUMAN1-76  1A:1-76
2UBIQUITIN_1PS00299 Ubiquitin domain signature.NEDD8_HUMAN27-52  1A:27-52

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002504951aENSE00001101093chr14:24701660-24701456205NEDD8_HUMAN1-661A:1-66
1.4ENST000002504954ENSE00002175755chr14:24687637-2468759048NEDD8_HUMAN7-22161A:7-2216
1.5aENST000002504955aENSE00002178617chr14:24687421-2468733983NEDD8_HUMAN23-50281A:23-5028
1.6eENST000002504956eENSE00001549615chr14:24686429-24686058372NEDD8_HUMAN50-81321A:50-7627

(-) 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 NEDD8_HUMAN | Q15843 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:76
                                    10        20        30        40        50        60        70      
           NEDD8_HUMAN    1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG 76
               SCOP domains d2ko3a_ A: Nedd8                                                             SCOP domains
               CATH domains 2ko3A00 A:1-76                                                               CATH domains
               Pfam domains -----ubiquitin-2ko3A01 A:6-74                                             -- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.....eeeee..ee.....hhhhhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) UBIQUITIN_2  PDB: A:1-76 UniProt: 1-76                                       PROSITE (1)
                PROSITE (2) --------------------------UBIQUITIN_1  PDB: A:27-52 ------------------------ PROSITE (2)
           Transcript 1 (1) 1.1a  Exon 1.4        Exon 1.5a  PDB: A:23-50     -------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.6e  PDB: A:50-76     Transcript 1 (2)
                  2ko3 A  1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG 76
                                    10        20        30        40        50        60        70      

   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  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (14, 14)

NMR Structure(hide GO term definitions)
Chain A   (NEDD8_HUMAN | Q15843)
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:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0009653    anatomical structure morphogenesis    The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
    GO:0045116    protein neddylation    Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0014070    response to organic cyclic compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0007179    transforming growth factor beta receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0006511    ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
    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: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
        NEDD8_HUMAN | Q158431ndd 1r4m 1r4n 1xt9 2bkr 2n7k 2nvu 3dbh 3dbl 3dbr 3dqv 3gzn 4f8c 4fbj 4hcp 4p5o

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