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(-) Description

Authors :  W. Dang, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Mar 06  (Deposition) - 30 Sep 06  (Release) - 24 Feb 09  (Revision)
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Thump Domain, Thump Domain-Containing Protein 1, 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 :  W. Dang, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of The Thump Domain Of Thump Domain-Containing Protein 1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP050905-19
    Expression System Vector TypePLASMID
    FragmentTHUMP DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 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 2DIR)

(-) Sites  (0, 0)

(no "Site" information available for 2DIR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Ala A:28 -Pro A:29

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
1THUMPPS51165 THUMP domain profile.THUM1_HUMAN147-254  1A:6-92

(-) Exons   (3, 3)

NMR Structure (3, 3)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3ENST000003960833ENSE00000676086chr16:20749278-20749030249THUM1_HUMAN136-219841A:6-57 (gaps)54
1.4cENST000003960834cENSE00001523808chr16:20748608-207449913618THUM1_HUMAN219-3531351A:57-98 (gaps)66

(-) 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:98
 aligned with THUM1_HUMAN | Q9NXG2 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:198
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276        
               SCOP domains -----------------------------------------------------------------------------------d2dira1 A:8-92 THUMP domain-containing protein 1                                     ------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------THUMP  PDB: A:6-92 UniProt: 147-254                                                                         ------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:1-5 UniProt: 78-136 [INCOMPLETE] ----------------------------------------------------------------------------------Exon 1.4c  PDB: A:57-98 (gaps) UniProt: 219-353 [INCOMPLETE]       Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.3  PDB: A:6-57 (gaps) UniProt: 136-219 [INCOMPLETE]                          ----------------------------------------------------------------- Transcript 1 (2)
                 2dir A   1 GSSGS--------------------------------------------------------------------------SG--KAFLEDMKKYAETFLEPWFKAPNKGTFQIVYKSRNNSHVNREEVIRELAGIVCTLNSENKVDLTNPQYTVVVEIIKAVCCLSVVKS-----------------GPS-------SG  98
                                |    -         -         -         -         -         -         -         6|  |    14        24        34        44        54        64        74        84        |-         -      | |-      | 
                                5                                                                          6|  8                                                                                   93                94 |      97 
                                                                                                            7                                                                                                          96         

   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 2DIR)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 5)

NMR Structure(hide GO term definitions)
Chain A   (THUM1_HUMAN | Q9NXG2)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0000154    rRNA modification    The covalent alteration of one or more nucleotides within an rRNA molecule to produce an rRNA molecule with a sequence that differs from that coded genetically.
cellular component
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.


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  Cis Peptide Bonds
    Ala A:28 - Pro A:29   [ RasMol ]  

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