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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RAN BINDING DOMAIN FROM THE NUCLEAR COMPLEX COMPONENT NUP2 FROM ASHBYA GOSSYPII
 
Authors :  V. N. Malashkevich, R. Toro, J. M. Sauder, S. K. Burley, S. C. Almo, New Y Research Center For Structural Genomics (Nysgxrc)
Date :  05 Aug 10  (Deposition) - 18 Aug 10  (Release) - 18 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Protein Structure Initiative, New York Structural Genomix Research Consortium, Nysgxrc, Psi-2, New York Sgx Research Center For Structural Genomics, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. N. Malashkevich, R. Toro, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of The Ran Binding Domain From The Nuclea Complex Component Nup2 From Ashbya Gossypii
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ABR034WP
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidBC-PSGX3(BC)
    Expression System StrainBL21(DE3)CODON+RIL
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL RESIDUES 497-615
    GeneABR034W, AGOS_ABR034W
    MutationYES
    Organism CommonYEAST
    Organism ScientificASHBYA GOSSYPII
    Organism Taxid33169
    StrainTCC 10895

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:65 , THR A:66 , ILE A:89BINDING SITE FOR RESIDUE GOL A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OAN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OAN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OAN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OAN)

(-) Exons   (0, 0)

(no "Exon" information available for 3OAN)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:116
 aligned with Q75DJ0_ASHGO | Q75DJ0 from UniProtKB/TrEMBL  Length:613

    Alignment length:116
                                                                                                                                            613    
                                   508       518       528       538       548       558       568       578       588       598       608    | 
         Q75DJ0_ASHGO   499 ENEEVLFCEKAKLLIFDSDTKGYTSRGVGELKLLRKKDDKGKVRVLCRSEGMGHVLLNTSVVKSFKYQPIDADNENLIKWPIITDGKLETFIIKVKQKADGRRLVGAVADAQQAM-   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Ran_BP1-3oanA01 A:8-121                                                                                           -- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeee....eeeeeeeeeeeeeee..eeeeeeeeeee.....eeeeee.......ee.......eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3oan A   8 ENEEVLFCEKAKLLIFDSDTKGYTSRGVGELKLLRKKDDKGKVRVLmRSEGmGHVLLNTSVVKSFKYQPIDADNENLIKWPIITDGKLETFIIKVKQKADGRRLVGAVADAQQAmE 123
                                    17        27        37        47      | 57 |      67        77        87        97       107       117    | 
                                                                         54-MSE|                                                            122-MSE
                                                                              59-MSE                                                            

   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 3OAN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OAN)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PH (111)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q75DJ0_ASHGO | Q75DJ0)
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:0005487    nucleocytoplasmic transporter activity    Enables the directed movement of substances between the nucleus and the cytoplasm of a cell.
biological process
    GO:0006607    NLS-bearing protein import into nucleus    The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0006405    RNA export from nucleus    The directed movement of RNA from the nucleus to the cytoplasm.
    GO:0030466    chromatin silencing at silent mating-type cassette    Repression of transcription at silent mating-type loci by alteration of the structure of chromatin.
    GO:0006348    chromatin silencing at telomere    Repression of transcription of telomeric DNA by altering the structure of chromatin.
    GO:0046907    intracellular transport    The directed movement of substances within a cell.
    GO:0031990    mRNA export from nucleus in response to heat stress    The directed movement of mRNA from the nucleus to the cytoplasm during a heat stimulus, a temperature stimulus above the optimal temperature for the organism; in particular, a process that enables an organism withstand exposure to temperatures that would otherwise lethally impair poly(A)+ mRNA-nucleus export.
    GO:0035392    maintenance of chromatin silencing at telomere    The maintenance of chromatin in a transcriptionally silent state such as heterochromatin at the telomere.
    GO:0033132    negative regulation of glucokinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of glucokinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a glucose molecule.
    GO:0070481    nuclear-transcribed mRNA catabolic process, non-stop decay    The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that is lacking a stop codon.
    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:0006611    protein export from nucleus    The directed movement of a protein from the nucleus into the cytoplasm.
    GO:0000061    protein import into nucleus, substrate release    A protein complex disassembly process that contributes to protein import into the nucleus, and that results in the dissociation of the cargo protein and the carrier (such as an importin alpha/beta heterodimer) from each other and from the nuclear pore complex.
    GO:0036228    protein localization to nuclear inner membrane    A process in which a protein is transported to, or maintained in, a location within the nuclear inner membrane.
    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:0006612    protein targeting to membrane    The process of directing proteins towards a membrane, usually using signals contained within the protein.
    GO:0090526    regulation of gluconeogenesis involved in cellular glucose homeostasis    Any process that modulates the frequency, rate or extent of gluconeogenesis as an integral part of cellular glucose homeostasis.
    GO:0000972    transcription-dependent 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. In S. cerevisiae, this process involves cis-acting DNA sequences such as the TATA box and upstream activating sequence (UAS) elements, trans-acting transcriptional activators, and also the 3'-UTR of the transcript.
cellular component
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005875    microtubule associated complex    Any multimeric complex connected to a microtubule.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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: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: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: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/TrEMBL
        Q75DJ0_ASHGO | Q75DJ03n7c

(-) Related Entries Specified in the PDB File

3n7c RELATED ID: NYSGXRC-15002C RELATED DB: TARGETDB