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(-) Description

Title :  SOLUTION STRUCTURE OF THE THIRD COLD-SHOCK DOMAIN OF THE HUMAN KIAA0885 PROTEIN (UNR PROTEIN)
 
Authors :  A. K. Goroncy, T. Kigawa, S. Koshiba, N. Kobayashi, N. Tochio, M. Inoue, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative
Date :  17 May 05  (Deposition) - 17 Nov 05  (Release) - 01 Sep 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Cell-Free Protein Synthesis, Beta-Barrel, Translational Regulation, Rna Chaperone, Rna/Dna Binding, Qb Fold, Greek-Key Topology, Unr Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. K. Goroncy, S. Koshiba, N. Tochio, T. Tomizawa, M. Inoue, S. Watanabe, T. Harada, A. Tanaka, O. Ohara, T. Kigawa, S. Yokoyama
The Nmr Solution Structures Of The Five Constituent Cold-Shock Domains (Csd) Of The Human Unr (Upstream Of N-Ras) Protein.
J. Struct. Funct. Genom. V. 11 181 2010
PubMed-ID: 20213426  |  Reference-DOI: 10.1007/S10969-010-9081-Z

(-) Compounds

Molecule 1 - UNR PROTEIN
    ChainsA
    EngineeredYES
    Expression System PlasmidP040114-41
    Expression System Vector TypePLASMID
    FragmentTHIRD COLD-SHOCK DOMAIN
    GeneUNR
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTESIS
    SynonymN-RAS UPSTREAM GENE PROTEIN

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1X65)

(-) Sites  (0, 0)

(no "Site" information available for 1X65)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X65)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X65)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X65)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COLD_SHOCKPS00352 'Cold-shock' domain signature.CSDE1_HUMAN37-56
197-216
360-379
530-549
  1-
-
A:20-39
-
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COLD_SHOCKPS00352 'Cold-shock' domain signature.CSDE1_HUMAN37-56
197-216
360-379
530-549
  1-
-
A:20-39
-

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2hENST000003585282hENSE00001828752chr1:115300585-11530054640CSDE1_HUMAN-00--
1.4bENST000003585284bENSE00001337441chr1:115292828-115292442387CSDE1_HUMAN-00--
1.8cENST000003585288cENSE00001713511chr1:115282511-115282313199CSDE1_HUMAN1-67670--
1.9bENST000003585289bENSE00001151258chr1:115280693-115280584110CSDE1_HUMAN67-103370--
1.10ENST0000035852810ENSE00000784321chr1:115280184-11528009293CSDE1_HUMAN104-134310--
1.11ENST0000035852811ENSE00002166908chr1:115279476-11527937998CSDE1_HUMAN135-167330--
1.12ENST0000035852812ENSE00001151239chr1:115277144-11527706382CSDE1_HUMAN167-194280--
1.13ENST0000035852813ENSE00000800122chr1:115276738-115276610129CSDE1_HUMAN195-237430--
1.14bENST0000035852814bENSE00000784325chr1:115276478-115276353126CSDE1_HUMAN238-279420--
1.15ENST0000035852815ENSE00000800120chr1:115275437-115275225213CSDE1_HUMAN280-350711A:1-10 (gaps)51
1.16ENST0000035852816ENSE00001386496chr1:115273269-115273129141CSDE1_HUMAN351-397471A:11-5747
1.17ENST0000035852817ENSE00000784333chr1:115273043-115272879165CSDE1_HUMAN398-452551A:58-89 (gaps)52
1.18ENST0000035852818ENSE00000800117chr1:115269711-115269604108CSDE1_HUMAN453-488360--
1.19aENST0000035852819aENSE00001450278chr1:115269007-115268832176CSDE1_HUMAN489-547590--
1.20ENST0000035852820ENSE00001151209chr1:115267954-115267842113CSDE1_HUMAN547-585390--
1.21bENST0000035852821bENSE00001151205chr1:115266623-115266504120CSDE1_HUMAN585-625410--
1.22bENST0000035852822bENSE00001151196chr1:115263338-115263160179CSDE1_HUMAN625-684600--
1.23ENST0000035852823ENSE00001196939chr1:115262363-115262200164CSDE1_HUMAN685-739550--
1.24bENST0000035852824bENSE00000784340chr1:115261366-115261234133CSDE1_HUMAN739-783450--
1.25fENST0000035852825fENSE00001374597chr1:115260837-1152595381300CSDE1_HUMAN784-798150--

(-) 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:89
 aligned with CSDE1_HUMAN | O75534 from UniProtKB/Swiss-Prot  Length:798

    Alignment length:150
                                   309       319       329       339       349       359       369       379       389       399       409       419       429       439       449
          CSDE1_HUMAN   300 GDKDTKSKVTLLEGDHVRFNISTDRRDKLERATNIEVLSNTFQFTNEAREMGVIAAMRDGFGFIKCVDRDVRMFFHFSEILDGNQLHIADEVEFTVVPDMLSAQRNHAIRIKKLPKGTVSFHSHSDHRFLGTVEKEATFSNPKTTSPNKG 449
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------------------------------------------------CSD-1x65A01 A:9-73                                               ------------------------------------ Pfam domains
         Sec.struct. author ....-----------------------------------------....eeeeeee......eeee...........hhhhhh........eee.................ee............--------------------..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------COLD_SHOCK          ---------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.15  PDB: A:1-10 (gaps) UniProt: 280-350     Exon 1.16  PDB: A:11-57 UniProt: 351-397       Exon 1.17  PDB: A:58-89 (gaps) UniProt: 398-452      Transcript 1
                 1x65 A   1 GSSG-----------------------------------------SSGREMGVIAAMRDGFGFIKCVDRDVRMFFHFSEILDGNQLHIADEVEFTVVPDMLSAQRNHAIRIKKLPKGTVSFHSHS--------------------GPSSG  89
                               |     -         -         -         -     |   9        19        29        39        49        59        69        79    |    -         -     |  89
                               4                                         5                                                                             84                   85    

   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 1X65)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1X65)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: OB (224)

(-) Gene Ontology  (12, 12)

NMR Structure(hide GO term definitions)
Chain A   (CSDE1_HUMAN | O75534)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0008584    male gonad development    The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
    GO:0070966    nuclear-transcribed mRNA catabolic process, no-go decay    The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA with stalls in translation elongation.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0070937    CRD-mediated mRNA stability complex    A protein complex that binds to, and promotes stabilization of, mRNA molecules containing the coding region instability determinant (CRD). In human, it may consist of IGF2BP1, HNRNPU, SYNCRIP/HNRNPQ, YBX1, and DHX9.
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CSDE1_HUMAN | O755341wfq 2ytv 2ytx 2yty

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