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(-) Description

Title :  ZINC-FINGER 2 OF NUP153
 
Authors :  J. A. Bangert, N. Schrader, I. R. Vetter, R. Stoll
Date :  31 Jan 08  (Deposition) - 01 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Zinc-Finger, Dna-Binding, Metal-Binding, Mrna Transport, Nuclear Pore Complex, Nucleus, Phosphoprotein, Protein Transport, Translocation, Transport, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Schrader, C. Koerner, K. Koessmeier, J. A. Bangert, A. Wittinghofer, R. Stoll, I. R. Vetter
The Crystal Structure Of The Ran-Nup153Znf2 Complex: A General Ran Docking Site At The Nuclear Pore Complex.
Structure V. 16 1116 2008
PubMed-ID: 18611384  |  Reference-DOI: 10.1016/J.STR.2008.03.014
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEAR PORE COMPLEX PROTEIN NUP153
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-4T1
    Expression System Vector TypePLASMID
    FragmentRANBP2-TYPE 2 DOMAIN (UNP RESIDUES 703-755)
    GeneNUP153
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    SynonymNUCLEOPORIN NUP153, 153 KDA NUCLEOPORIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:7BINDING SITE FOR RESIDUE ZN A 54

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2K0C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2K0C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2K0C)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_RANBP2_2PS50199 Zinc finger RanBP2 type profile.NU153_RAT657-687
721-750
789-818
846-875
  1-
A:1-30
-
-
2ZF_RANBP2_1PS01358 Zinc finger RanBP2-type signature.NU153_RAT662-681
725-744
793-812
850-869
  1-
A:5-24
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 2K0C)

(-) 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:35
 aligned with NU153_RAT | P49791 from UniProtKB/Swiss-Prot  Length:1468

    Alignment length:35
                                   730       740       750     
            NU153_RAT   721 AIGTWDCDTCLVQNKPEAVKCVACETPKPGTGVKR 755
               SCOP domains d2k0ca_ A:                          SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains -zf-RanBP-2k0cA01 A:2-30      ----- Pfam domains
         Sec.struct. author ....eee....eee..................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                PROSITE (1) ZF_RANBP2_2  PDB: A:1-30      ----- PROSITE (1)
                PROSITE (2) ----ZF_RANBP2_1         ----------- PROSITE (2)
                 Transcript ----------------------------------- Transcript
                 2k0c A   1 AIGTWDCDTCLVQNKPEAVKCVACETPKPGTGVKR  35
                                    10        20        30     

   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  (0, 0)

(no "CATH Domain" information available for 2K0C)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (27, 27)

NMR Structure(hide GO term definitions)
Chain A   (NU153_RAT | P49791)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008536    Ran GTPase binding    Interacting selectively and non-covalently with Ran, a conserved Ras-like GTP-binding protein, implicated in nucleocytoplasmic transport, cell cycle progression, spindle assembly, nuclear organization and nuclear envelope (NE) assembly.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0043495    protein anchor    Interacting selectively and non-covalently with both a protein or protein complex and a membrane, in order to maintain the localization of the protein at a specific membrane location.
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    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:0046832    negative regulation of RNA export from nucleus    Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of RNA from the nucleus into the cytoplasm.
    GO:0051292    nuclear pore complex assembly    The aggregation, arrangement and bonding together of a set of components to form a nuclear pore complex.
    GO:0006913    nucleocytoplasmic transport    The directed movement of molecules between the nucleus and the cytoplasm.
    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: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:0005642    annulate lamellae    Stacks of endoplasmic reticulum (ER) membranes containing a high density of nuclear pores, thought to form from excess nuclear membrane components, that have been described in a number of different cells. Annulate lamellar membranes are continuous with and embedded within the ER.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0042405    nuclear inclusion body    An intranuclear focus at which aggregated proteins have been sequestered.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0034399    nuclear periphery    The portion of the nuclear lumen proximal to the inner nuclear membrane.
    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:0044615    nuclear pore nuclear basket    A filamentous, cage-like assembly on the nuclear face of the nuclear pore complex (NPC). In S. cerevisiae, Mlp1p and Mlp2p are two major components of the NPC nuclear basket. In vertebrates, Tpr is a major component.
    GO:1990875    nucleoplasmic side of nuclear pore    The side of the nuclear pore complex (NPC) that faces the nucleoplasm.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NU153_RAT | P497913ch5 3gj3 3gj4 3gj5 3gj6 3gj7 3gj8

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