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(-) Description

Title :  SOLUTION STRUCTURE OF THE RANBD1 DOMAIN FROM HUMAN NUCLEOPORIN 50 KDA
 
Authors :  H. P. Zhang, C. Kurosaki, M. Yoshida, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  09 Feb 07  (Deposition) - 14 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Ranbp Domain, Nucleoporin 50 Kda, Nuclear Pore-Associated Protein 60 Kda-Like, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. P. Zhang, C. Kurosaki, M. Yoshida, F. Hayashi, S. Yokoyama
Solution Structure Of The Ranbd1 Domain From Human Nucleoporin 50 Kda
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEOPORIN 50 KDA
    Chains: A
    Engineered: YES
    Expression System Plasmid: P060320-24
    Expression System Vector Type: PLASMID
    Fragment: RANBP DOMAIN
    Gene: NUP50, NPAP60L, PRO1146
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL FREE PROTEIN SYNTHESIS
    Synonym: NUCLEAR PORE-ASSOCIATED PROTEIN 60 KDA-LIKE

 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 2EC1)

(-) Sites  (0, 0)

(no "Site" information available for 2EC1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EC1)

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Asn A:88 -Pro A:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EC1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EC1)

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003476351aENSE00001185148chr22:45559722-45560177456NUP50_HUMAN-00--
1.5dENST000003476355dENSE00002142994chr22:45564049-4556412779NUP50_HUMAN1-23230--
1.7cENST000003476357cENSE00001748959chr22:45567481-4556756484NUP50_HUMAN24-51280--
1.8cENST000003476358cENSE00000657043chr22:45571775-45571961187NUP50_HUMAN52-114630--
1.9eENST000003476359eENSE00001660061chr22:45574119-45574781663NUP50_HUMAN114-3352220--
1.11ENST0000034763511ENSE00001697601chr22:45577167-4557724882NUP50_HUMAN335-362281A:8-1912
1.12bENST0000034763512bENSE00001797834chr22:45579283-45579401119NUP50_HUMAN362-402411A:19-5941
1.12hENST0000034763512hENSE00001300233chr22:45580334-455838923559NUP50_HUMAN402-468671A:59-12567

(-) 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:118
 aligned with NUP50_HUMAN | Q9UKX7 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:118
                                   360       370       380       390       400       410       420       430       440       450       460        
          NUP50_HUMAN   351 EVKEEDAFYSKKCKLFYKKDNEFKEKGIGTLHLKPTANQKTQLLVRADTNLGNILLNVLIPPNMPCTRTGKNNVLIVCVPNPPIDEKNATMPVTMLIRVKTSEDADELHKILLEKKDA 468
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeee..........ee......ee.....eeeeee..............eeeeee..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11   ---------------------------------------Exon 1.12h  PDB: A:59-125 UniProt: 402-468                          Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.12b  PDB: A:19-59 UniProt: 362-402------------------------------------------------------------------ Transcript 1 (2)
                 2ec1 A   8 EVKEEDAFYSKKCKLFYKKDNEFKEKGIGTLHLKPTANQKTQLLVRADTNLGNILLNVLIPPNMPCTRTGKNNVLIVCVPNPPIDEKNATMPVTMLIRVKTSEDADELHKILLEKKDA 125
                                    17        27        37        47        57        67        77        87        97       107       117
   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  (0, 0)

(no "SCOP Domain" information available for 2EC1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2EC1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EC1)

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (NUP50_HUMAN | Q9UKX7)
molecular function
    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: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:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0046907    intracellular transport    The directed movement of substances within a cell.
    GO:0075733    intracellular transport of virus    The directed movement of a virus, or part of a virus, within the host cell.
    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:0007077    mitotic nuclear envelope disassembly    The cell cycle process in which the controlled breakdown of the nuclear envelope during mitotic cell division occurs.
    GO:0006606    protein import into nucleus    The directed movement of a protein from the cytoplasm to the nucleus.
    GO:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
    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:1900034    regulation of cellular response to heat    Any process that modulates the frequency, rate or extent of cellular response to heat.
    GO:0010827    regulation of glucose transport    Any process that modulates the frequency, rate or extent of glucose transport. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006409    tRNA export from nucleus    The directed movement of tRNA from the nucleus to the cytoplasm.
    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.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019083    viral transcription    The process by which a viral genome, or part of a viral genome, is transcribed within the host cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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.

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    Asn A:88 - Pro A:89   [ RasMol ]  
 

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        NUP50_HUMAN | Q9UKX7: 3tj3

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