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(-) Description

Title :  NMR STRUCTURE OF THE UBX DOMAIN FROM P47
 
Authors :  X. Yuan, A. Shaw, X. Zhang, H. Kondo, J. Lally, P. S. Freemont, S. Matthews
Date :  19 Feb 01  (Deposition) - 29 Aug 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Ubiquitin Superfold, Ubx, Unusual N-Terminal Feature, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Yuan, A. Shaw, X. Zhang, H. Kondo, J. Lally, P. S. Freemont, S. Matthews
Solution Structure And Interaction Surface Of The C-Terminal Domain From P47: A Major P97-Cofactor Involved In Snare Disassembly.
J. Mol. Biol. V. 311 255 2001
PubMed-ID: 11478859  |  Reference-DOI: 10.1006/JMBI.2001.4864
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - P47
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPPRO-EX HTB
    Expression System StrainBL21 DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL DOMAIN(RESIDUES 282-370)
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1I42)

(-) Sites  (0, 0)

(no "Site" information available for 1I42)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I42)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1I42)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I42)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBXPS50033 UBX domain profile.NSF1C_RAT291-368  1A:291-368

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000116541ENSRNOE00000080778chr3:141799286-141799498213NSF1C_RAT1-35350--
1.2ENSRNOT000000116542ENSRNOE00000080974chr3:141801645-14180174298NSF1C_RAT36-68330--
1.3ENSRNOT000000116543ENSRNOE00000081202chr3:141806924-14180699875NSF1C_RAT68-93260--
1.5ENSRNOT000000116545ENSRNOE00000081435chr3:141809288-141809453166NSF1C_RAT93-148560--
1.6ENSRNOT000000116546ENSRNOE00000081642chr3:141810321-14181041393NSF1C_RAT149-179310--
1.7ENSRNOT000000116547ENSRNOE00000081878chr3:141811633-141811742110NSF1C_RAT180-216370--
1.8ENSRNOT000000116548ENSRNOE00000082111chr3:141812671-141812808138NSF1C_RAT216-262470--
1.9ENSRNOT000000116549ENSRNOE00000082354chr3:141821967-141822131165NSF1C_RAT262-317561A:282-31736
1.10ENSRNOT0000001165410ENSRNOE00000349261chr3:141823371-141823731361NSF1C_RAT317-370541A:317-37054

(-) 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:89
 aligned with NSF1C_RAT | O35987 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:89
                                   291       301       311       321       331       341       351       361         
            NSF1C_RAT   282 KASSSILINEAEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPNKELADENQTLKEANLLNAVIVQRLT 370
               SCOP domains d1i42a_ A: p47                                                                            SCOP domains
               CATH domains 1i42A00 A:282-370 Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee...eeeeeee....hhhhhhhhhhhhh.hhhhheeeee.......................eeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------UBX  PDB: A:291-368 UniProt: 291-368                                          -- PROSITE
           Transcript 1 (1) -----------------------------------Exon 1.10  PDB: A:317-370 UniProt: 317-370             Transcript 1 (1)
           Transcript 1 (2) Exon 1.9  PDB: A:282-317            ----------------------------------------------------- Transcript 1 (2)
                 1i42 A 282 KASSSILINEAEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPNKELADENQTLKEANLLNAVIVQRLT 370
                                   291       301       311       321       331       341       351       361         

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  - → Gap (green background, '-', border residues have a numbering label)
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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
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I42)

(-) Gene Ontology  (19, 19)

NMR Structure(hide GO term definitions)
Chain A   (NSF1C_RAT | O35987)
molecular function
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    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:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
biological process
    GO:0007030    Golgi organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus.
    GO:0061025    membrane fusion    The membrane organization process that joins two lipid bilayers to form a single membrane.
    GO:0031468    nuclear envelope reassembly    The reformation of the nuclear envelope following its breakdown in the context of a normal process.
    GO:0043161    proteasome-mediated 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 ubiquitin, and mediated by the proteasome.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005795    Golgi stack    The set of thin, flattened membrane-bounded compartments, called cisternae, that form the central portion of the Golgi complex. The stack usually comprises cis, medial, and trans cisternae; the cis- and trans-Golgi networks are not considered part of the stack.
    GO:1990730    VCP-NSFL1C complex    A protein complex between the ATPase VCP (p97) and its cofactor p47 (NSFL1C). In human, the protein complex consists of one homotrimer of NSFL1C/p47 per homohexamer of VCP/p97.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    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:0045111    intermediate filament cytoskeleton    Cytoskeletal structure made from intermediate filaments, typically organized in the cytosol as an extended system that stretches from the nuclear envelope to the plasma membrane. Some intermediate filaments run parallel to the cell surface, while others traverse the cytosol; together they form an internal framework that helps support the shape and resilience of the cell.
    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: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
        NSF1C_RAT | O359871jru 1s3s 1v92 1vaz

(-) Related Entries Specified in the PDB File

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