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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NTF2-LIKE DOMAIN OF THE DROSOPHILA MELANOGASTER RASPUTIN PROTEIN
 
Authors :  T. Vognsen, O. Kristensen
Date :  08 Nov 11  (Deposition) - 25 Apr 12  (Release) - 25 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.74
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ntf2-Like Fold, Ras Signaling, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Vognsen, O. Kristensen
Crystal Structure Of The Rasputin Ntf2-Like Domain From Drosophila Melanogaster.
Biochem. Biophys. Res. Commun. V. 420 188 2012
PubMed-ID: 22414690  |  Reference-DOI: 10.1016/J.BBRC.2012.02.140

(-) Compounds

Molecule 1 - RASPUTIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: NTF2-LIKE DOMAIN
    Gene: RIN, CG9412
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:37 , LYS A:118 , TYR A:120 , TYR A:121BINDING SITE FOR RESIDUE EPE A 201
2AC2SOFTWAREARG B:37 , LYS B:118 , TYR B:120 , TYR B:121BINDING SITE FOR RESIDUE EPE B 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3UJM)

(-) 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:117
 aligned with Q9NH72_DROME | Q9NH72 from UniProtKB/TrEMBL  Length:690

    Alignment length:117
                                    23        33        43        53        63        73        83        93       103       113       123       
         Q9NH72_DROME    14 QSVGREFVRQYYTLLNKAPNHLHRFYNHNSSYIHGESKLVVGQREIHNRIQQLNFNDCHAKISQVDAQATLGNGVVVQVTGELSNDGQPMRRFTQTFVLAAQSPKKYYVHNDIFRYQ 130
               SCOP domains d3ujma_ A: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.....eehhhhhhhhhhhhh....eeeeeeeeeeeehhheeeeeeeeeee......eeeeeeeee.........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3ujm A  14 MSVGREFVRQYYTLLNKAPNHLHRFYNHNSSYIHGESKLVVGQREIHNRIQQLNFNDCHAKISQVDAQATLGNGVVVQVTGELSNDGQPMRRFTQTFVLAAQSPKKYYVHNDIFRYQ 130
                                    23        33        43        53        63        73        83        93       103       113       123       


Chain A from PDB  Type:PROTEIN  Length:117
 aligned with Q9VFT4_DROME | Q9VFT4 from UniProtKB/TrEMBL  Length:690

    Alignment length:117
                                    23        33        43        53        63        73        83        93       103       113       123       
         Q9VFT4_DROME    14 QSVGREFVRQYYTLLNKAPNHLHRFYNHNSSYIHGESKLVVGQREIHNRIQQLNFNDCHAKISQVDAQATLGNGVVVQVTGELSNDGQPMRRFTQTFVLAAQSPKKYYVHNDIFRYQ 130
               SCOP domains d3ujma_ A: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.....eehhhhhhhhhhhhh....eeeeeeeeeeeehhheeeeeeeeeee......eeeeeeeee.........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3ujm A  14 MSVGREFVRQYYTLLNKAPNHLHRFYNHNSSYIHGESKLVVGQREIHNRIQQLNFNDCHAKISQVDAQATLGNGVVVQVTGELSNDGQPMRRFTQTFVLAAQSPKKYYVHNDIFRYQ 130
                                    23        33        43        53        63        73        83        93       103       113       123       


Chain B from PDB  Type:PROTEIN  Length:117
 aligned with Q9NH72_DROME | Q9NH72 from UniProtKB/TrEMBL  Length:690

    Alignment length:117
                                    23        33        43        53        63        73        83        93       103       113       123       
         Q9NH72_DROME    14 QSVGREFVRQYYTLLNKAPNHLHRFYNHNSSYIHGESKLVVGQREIHNRIQQLNFNDCHAKISQVDAQATLGNGVVVQVTGELSNDGQPMRRFTQTFVLAAQSPKKYYVHNDIFRYQ 130
               SCOP domains d3ujmb_ B: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh....eeee.....eehhhhhhhhhhhhh....eeeeeeeeeeeehhheeeeeeeeeee......eeeeeeeeeee.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3ujm B  14 MSVGREFVRQYYTLLNKAPNHLHRFYNHNSSYIHGESKLVVGQREIHNRIQQLNFNDCHAKISQVDAQATLGNGVVVQVTGELSNDGQPMRRFTQTFVLAAQSPKKYYVHNDIFRYQ 130
                                    23        33        43        53        63        73        83        93       103       113       123       


Chain B from PDB  Type:PROTEIN  Length:117
 aligned with Q9VFT4_DROME | Q9VFT4 from UniProtKB/TrEMBL  Length:690

    Alignment length:117
                                    23        33        43        53        63        73        83        93       103       113       123       
         Q9VFT4_DROME    14 QSVGREFVRQYYTLLNKAPNHLHRFYNHNSSYIHGESKLVVGQREIHNRIQQLNFNDCHAKISQVDAQATLGNGVVVQVTGELSNDGQPMRRFTQTFVLAAQSPKKYYVHNDIFRYQ 130
               SCOP domains d3ujmb_ B: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh....eeee.....eehhhhhhhhhhhhh....eeeeeeeeeeeehhheeeeeeeeeee......eeeeeeeeeee.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3ujm B  14 MSVGREFVRQYYTLLNKAPNHLHRFYNHNSSYIHGESKLVVGQREIHNRIQQLNFNDCHAKISQVDAQATLGNGVVVQVTGELSNDGQPMRRFTQTFVLAAQSPKKYYVHNDIFRYQ 130
                                    23        33        43        53        63        73        83        93       103       113       123
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UJM)

(-) Gene Ontology  (19, 38)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9VFT4_DROME | Q9VFT4)
molecular function
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0007265    Ras protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
    GO:0001752    compound eye photoreceptor fate commitment    The process in which the developmental fate of a cell becomes restricted such that it will develop into a compound eye photoreceptor cell. A photoreceptor cell is a cell that responds to incident electromagnetic radiation. Different classes of photoreceptor have different spectral sensitivities and express different photosensitive pigments.
    GO:0008069    dorsal/ventral axis specification, ovarian follicular epithelium    Polarization of the ovarian follicle cells along the dorsal/ventral axis. An example of this process is found in Drosophila melanogaster.
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    GO:0045571    negative regulation of imaginal disc growth    Any process that stops, prevents, or reduces the frequency, rate or extent of imaginal disc growth.
    GO:0016318    ommatidial rotation    The process in which photoreceptors are arranged in ommatidia in the dorsal and ventral fields to be mirror images. The polarity is established in the imaginal discs concurrently with cell fate specification.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    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:0071013    catalytic step 2 spliceosome    A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs.
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0005811    lipid droplet    An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
    GO:0071011    precatalytic spliceosome    A spliceosomal complex that is formed by the recruitment of a preassembled U5-containing tri-snRNP to the prespliceosome. Although all 5 snRNPs are present, the precatalytic spliceosome is catalytically inactive. The precatalytic spliceosome includes many proteins in addition to those found in the associated snRNPs.

Chain A,B   (Q9NH72_DROME | Q9NH72)
molecular function
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0007265    Ras protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
    GO:0001752    compound eye photoreceptor fate commitment    The process in which the developmental fate of a cell becomes restricted such that it will develop into a compound eye photoreceptor cell. A photoreceptor cell is a cell that responds to incident electromagnetic radiation. Different classes of photoreceptor have different spectral sensitivities and express different photosensitive pigments.
    GO:0008069    dorsal/ventral axis specification, ovarian follicular epithelium    Polarization of the ovarian follicle cells along the dorsal/ventral axis. An example of this process is found in Drosophila melanogaster.
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    GO:0045571    negative regulation of imaginal disc growth    Any process that stops, prevents, or reduces the frequency, rate or extent of imaginal disc growth.
    GO:0016318    ommatidial rotation    The process in which photoreceptors are arranged in ommatidia in the dorsal and ventral fields to be mirror images. The polarity is established in the imaginal discs concurrently with cell fate specification.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    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:0071013    catalytic step 2 spliceosome    A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs.
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0005811    lipid droplet    An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
    GO:0071011    precatalytic spliceosome    A spliceosomal complex that is formed by the recruitment of a preassembled U5-containing tri-snRNP to the prespliceosome. Although all 5 snRNPs are present, the precatalytic spliceosome is catalytically inactive. The precatalytic spliceosome includes many proteins in addition to those found in the associated snRNPs.

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