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(-) Description

Title :  SOLUTION STRUCTURE OF THE YTH DOMAIN IN YTH DOMAIN-CONTAINING PROTEIN 2
 
Authors :  R. Endo, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Tarada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  05 Apr 07  (Deposition) - 09 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Yth Domain, 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 :  R. Endo, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Tarada, S. Yokoyama
Solution Structure Of The Yth Domain In Yth Domain-Containing Protein 2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - YTH DOMAIN-CONTAINING PROTEIN 2
    ChainsA
    EngineeredYES
    Expression System PlasmidP060508-16
    Expression System Vector TypePLASMID
    FragmentYTH DOMAIN
    GeneYTHDC2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS

 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 2YU6)

(-) Sites  (0, 0)

(no "Site" information available for 2YU6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YU6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YU6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_058003L1409QYTDC2_HUMANPolymorphism1132528AQ129Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1YTHPS50882 YTH domain profile.YTDC2_HUMAN1288-1418  1A:8-138

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000001618631aENSE00002083751chr5:112849380-112849779400YTDC2_HUMAN1-63630--
1.3ENST000001618633ENSE00001180477chr5:112850969-11285105991YTDC2_HUMAN63-93310--
1.5ENST000001618635ENSE00001180473chr5:112860678-112860874197YTDC2_HUMAN93-159670--
1.6bENST000001618636bENSE00001306353chr5:112862283-112862482200YTDC2_HUMAN159-225670--
1.7ENST000001618637ENSE00001260818chr5:112868576-112868742167YTDC2_HUMAN226-281560--
1.8ENST000001618638ENSE00001260806chr5:112870002-112870104103YTDC2_HUMAN281-315350--
1.9ENST000001618639ENSE00001260796chr5:112871339-112871495157YTDC2_HUMAN316-368530--
1.10ENST0000016186310ENSE00001375927chr5:112874771-112874878108YTDC2_HUMAN368-404370--
1.11ENST0000016186311ENSE00001389542chr5:112876665-112876813149YTDC2_HUMAN404-453500--
1.12ENST0000016186312ENSE00001364452chr5:112878065-112878200136YTDC2_HUMAN454-499460--
1.13ENST0000016186313ENSE00001363942chr5:112884238-112884364127YTDC2_HUMAN499-541430--
1.14ENST0000016186314ENSE00001371690chr5:112884652-11288471766YTDC2_HUMAN541-563230--
1.15ENST0000016186315ENSE00001383801chr5:112888878-112889056179YTDC2_HUMAN563-623610--
1.16ENST0000016186316ENSE00001082549chr5:112889287-11288938397YTDC2_HUMAN623-655330--
1.17ENST0000016186317ENSE00001082542chr5:112889464-11288955188YTDC2_HUMAN655-684300--
1.18ENST0000016186318ENSE00001082539chr5:112889639-11288971981YTDC2_HUMAN685-711270--
1.19aENST0000016186319aENSE00001343036chr5:112891749-11289183183YTDC2_HUMAN712-739280--
1.20aENST0000016186320aENSE00001326602chr5:112896777-112896882106YTDC2_HUMAN739-774360--
1.21ENST0000016186321ENSE00000760310chr5:112899070-112899189120YTDC2_HUMAN775-814400--
1.22ENST0000016186322ENSE00000588976chr5:112899556-112899828273YTDC2_HUMAN815-905910--
1.23bENST0000016186323bENSE00000760317chr5:112901590-112901716127YTDC2_HUMAN906-948430--
1.24ENST0000016186324ENSE00000760318chr5:112902789-112902994206YTDC2_HUMAN948-1016690--
1.25ENST0000016186325ENSE00000760319chr5:112903351-112903546196YTDC2_HUMAN1017-1082660--
1.26bENST0000016186326bENSE00000760320chr5:112915283-112915392110YTDC2_HUMAN1082-1118370--
1.27bENST0000016186327bENSE00000364322chr5:112917114-112917406293YTDC2_HUMAN1119-1216980--
1.27cENST0000016186327cENSE00000760321chr5:112919999-112920176178YTDC2_HUMAN1216-1275601A:1-77
1.28aENST0000016186328aENSE00000760322chr5:112926738-112926941204YTDC2_HUMAN1276-1343681A:8-6356
1.29aENST0000016186329aENSE00000760323chr5:112927693-112927875183YTDC2_HUMAN1344-1404611A:64-12461
1.29dENST0000016186329dENSE00000890208chr5:112929000-11292908788YTDC2_HUMAN1405-1430261A:125-14117
1.29fENST0000016186329fENSE00000890209chr5:112929179-1129309811803YTDC2_HUMAN-00--

(-) 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:141
 aligned with YTDC2_HUMAN | Q9H6S0 from UniProtKB/Swiss-Prot  Length:1430

    Alignment length:154
                                  1277      1287      1297      1307      1317      1327      1337      1347      1357      1367      1377      1387      1397      1407      1417    
         YTDC2_HUMAN   1268 PSPPSSGKGSKSPSPRPNMPVRYFIMKSSNLRNLEISQQKGIWSTTPSNERKLNRAFWESSIVYLVFSVQGSGHFQGFSRMSSEIGREKSQDWGSAGLGGVFKVEWIRKESLPFQFAHHLLNPWNDNKKVQISRDGQELEPLVGEQLLQLWERL 1421
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------YTH-2yu6A01 A:8-141                                                                                                                    Pfam domains
         Sec.struct. author .......-------------.eeeeeee...hhhhhhhh..eee.....hhhhhhhhhh...eeeeeee....ee.eeeee...................eeeeeeee...eehhhh...ee.....ee.......eee...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------Q------------ SAPs(SNPs)
                    PROSITE --------------------YTH  PDB: A:8-138 UniProt: 1288-1418                                                                                               --- PROSITE
               Transcript 1 1.27c   Exon 1.28a  PDB: A:8-63 UniProt: 1276-1343 [INCOMPLETE]             Exon 1.29a  PDB: A:64-124 UniProt: 1344-1404                 Exon 1.29d        Transcript 1
                2yu6 A    1 GSSGSSG-------------VRYFIMKSSNLRNLEISQQKGIWSTTPSNERKLNRAFWESSIVYLVFSVQGSGHFQGFSRMSSEIGREKSQDWGSAGLGGVFKVEWIRKESLPFQFAHHLLNPWNDNKKVQISRDGQELEPQVGEQLLQLWERL  141
                                  |  -         -|       17        27        37        47        57        67        77        87        97       107       117       127       137    
                                  7             8                                                                                                                                     

   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 2YU6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YU6)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: PUA (42)

(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A   (YTDC2_HUMAN | Q9H6S0)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004004    ATP-dependent RNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix.
    GO:1990247    N6-methyladenosine-containing RNA binding    Interacting selectively and non-covalently with an RNA molecule modified by N6-methyladenosine (m6A), a modification present at internal sites of mRNAs and some non-coding RNAs.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0070063    RNA polymerase binding    Interacting selectively and non-covalently with an RNA polymerase molecule or complex.
    GO:0008186    RNA-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of RNA, and it drives another reaction.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    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:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0044829    positive regulation by host of viral genome replication    A process in which a host organism activates or increases the frequency, rate or extent of viral genome replication.
    GO:0070555    response to interleukin-1    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-1 stimulus.
    GO:0034612    response to tumor necrosis factor    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    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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