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(-) Description

Title :  MULTIPLE CONFORMATIONS IN THE LIGAND-BINDING SITE OF THE YEAST NUCLEAR PORE TARGETING DOMAIN OF NUP116P
 
Authors :  M. A. Robinson, S. Park, Z-Y. J. Sun, P. Silver, G. Wagner, J. Hogle
Date :  01 Aug 05  (Deposition) - 16 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (15x)
Keywords :  Beta Sandwich, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. A. Robinson, S. Park, Z-Y. J. Sun, P. A. Silver, G. Wagner, J. M. Hogle
Multiple Conformations In The Ligand-Binding Site Of The Yeast Nuclear Pore-Targeting Domain Of Nup116P
J. Biol. Chem. V. 280 35723 2005
PubMed-ID: 16105837  |  Reference-DOI: 10.1074/JBC.M505068200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FRAGMENT OF NUCLEOPORIN NUP116/NSP116
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDEST 15
    Expression System StrainBL21-CODONPLUS-RIL
    Expression System Taxid562
    Expression System Vector TypeGATEWAY
    FragmentC-TERMINAL DOMAIN, RESIDUES 967-1113
    GeneNUP116, NSP116
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    Other DetailsFRAGMENT INTERACTING WITH NUP82 NPC SUBCOMPLEX
    SynonymNUP116P;
NUCLEAR PORE PROTEIN NUP116/NSP116

 Structural Features

(-) Chains, Units

  
NMR Structure (15x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2AIV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 15)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15Ser A:9 -Pro A:10

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUP_CPS51434 NUP C-terminal domain profile.NU116_YEAST967-1109  1A:3-145

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YMR047C1YMR047C.1XIII:366704-3633633342NU116_YEAST1-111311131A:1-149 (gaps)207

(-) 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:149
 aligned with NU116_YEAST | Q02630 from UniProtKB/Swiss-Prot  Length:1113

    Alignment length:207
                                   916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076      1086      1096      1106       
         NU116_YEAST    907 GERMVLSSKNDGEDSATKHHSRNMDEENKENVADLQKQEYSEDDKKAVFADVAEKDASFINENYYISPSLDTLSSYSLLQLRKVPHLVVGHKSYGKIEFLEPVDLAGIPLTSLGGVIITFEPKTCIIYANLPNRPKRGEGINVRARITCFNCYPVDKSTRKPIKDPNHQLVKRHIERLKKNPNSKFESYDADSGTYVFIVNHAAEQT 1113
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..----------------------------------------------------------........hhhhhhh.hhhhhhh...eeee.....eeee.........hhhhhh....ee....ee..................eeeee....................hhhhhhhhhhhh...eeeee......eeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------NUP_C  PDB: A:3-145 UniProt: 967-1109                                                                                                          ---- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-149 (gaps) UniProt: 1-1113 [INCOMPLETE]                                                                                                                                                      Transcript 1
                2aiv A    1 GP----------------------------------------------------------NENYYISPSLDTLSSYSLLQLRKVPHLVVGHKSYGKIEFLEPVDLAGIPLTSLGGVIITFEPKTCIIYANLPNRPKRGEGINVRARITCFNCYPVDKSTRKPIKDPNHQLVKRHIERLKKNPNSKFESYDADSGTYVFIVNHAAEQT  149
                             |       -         -         -         -         -         -|       12        22        32        42        52        62        72        82        92       102       112       122       132       142       
                             2                                                          3                                                                                                                                                  

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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  (0, 0)

(no "SCOP Domain" information available for 2AIV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (NU116_YEAST | Q02630)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0008139    nuclear localization sequence binding    Interacting selectively and non-covalently with a nuclear localization sequence, a specific peptide sequence that acts as a signal to localize the protein within the nucleus.
    GO:0005487    nucleocytoplasmic transporter activity    Enables the directed movement of substances between the nucleus and the cytoplasm of a cell.
    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:0017056    structural constituent of nuclear pore    The action of a molecule that contributes to the structural integrity of the nuclear pore complex.
biological process
    GO:0006406    mRNA export from nucleus    The directed movement of mRNA from the nucleus to the cytoplasm.
    GO:0051028    mRNA transport    The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006999    nuclear pore organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear pore.
    GO:0016973    poly(A)+ mRNA export from nucleus    The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm.
    GO:0000973    posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery    The chromosome organization process in which the DNA sequence containing a gene transcribed by RNA polymerase II is maintained in a specific location at the nuclear periphery even after transcription has been repressed.
    GO:0006606    protein import into nucleus    The directed movement of a protein from the cytoplasm to the nucleus.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0000055    ribosomal large subunit export from nucleus    The directed movement of a ribosomal large subunit from the nucleus into the cytoplasm.
    GO:0006409    tRNA export from nucleus    The directed movement of tRNA from the nucleus to the cytoplasm.
    GO:0034398    telomere tethering at nuclear periphery    The process in which a telomere is maintained in a specific location at the nuclear periphery.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0005643    nuclear pore    Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
    GO:0044613    nuclear pore central transport channel    The central substructure of the nuclear pore complex (NPC), through which nucleocytoplasmic transport of RNAs, proteins and small molecules occurs. The central transport channel is filled with FG-nucleoporins, which form a selective barrier and provide a series of binding sites for transporter proteins. Characterized S. cerevisiae FG-nucleoporins include Nup159p, Nup145Np, Nup116p, Nup100p, Nsp1p, Nup57p, Nup49p, Nup42p, Nup53p, Nup59p/Asm4p, Nup60p and Nup1. Characterized vertebrate FG-nucleoporins include Nup214, Nup98, Nup62, Nup54, Nup58/45, NLP1, and Nup153.
    GO:0044614    nuclear pore cytoplasmic filaments    Filamentous extensions on cytoplasmic face of the nuclear pore complex (NPC). In S. cerevisiae, Nup159p, Nup82p, and Nup42p contribute to the cytoplasmic filaments. In vertebrates, Nup358 is a major component.
    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
        NU116_YEAST | Q026301o6p 3pbp

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