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(-) Description

Title :  SOLUTION STRUCTURE OF THE S1 RNA BINDING DOMAIN OF HUMAN ATP-DEPENDENT RNA HELICASE DHX8
 
Authors :  S. Suzuki, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Mar 07  (Deposition) - 02 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  S1 Domain, Ob-Fold, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Suzuki, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of The S1 Rna Binding Domain Of Human Atp-Dependent Rna Helicase Dhx8
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ATP-DEPENDENT RNA HELICASE DHX8
    ChainsA
    EC Number3.6.1.-
    EngineeredYES
    Expression System PlasmidP060919-24
    Expression System Vector TypePLASMID
    FragmentS1 DOMAIN
    GeneDHX8
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymDEAH BOX PROTEIN 8, RNA HELICASE HRH1

 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 2EQS)

(-) Sites  (0, 0)

(no "Site" information available for 2EQS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1S1PS50126 S1 domain profile.DHX8_HUMAN265-336  1A:265-336

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002624151ENSE00001280005chr17:41561334-41561553220DHX8_HUMAN1-50500--
1.2ENST000002624152ENSE00000897775chr17:41566817-4156690286DHX8_HUMAN50-78290--
1.3ENST000002624153ENSE00000897782chr17:41567759-4156783173DHX8_HUMAN79-103250--
1.4ENST000002624154ENSE00000897789chr17:41568533-4156861886DHX8_HUMAN103-131290--
1.5ENST000002624155ENSE00000897797chr17:41569551-41569660110DHX8_HUMAN132-168370--
1.6ENST000002624156ENSE00001133080chr17:41570049-41570408360DHX8_HUMAN168-2881211A:253-288 (gaps)63
1.7ENST000002624157ENSE00001133071chr17:41570813-41570957145DHX8_HUMAN288-336491A:288-33649
1.8ENST000002624158ENSE00001133060chr17:41571051-41571254204DHX8_HUMAN337-404681A:337-35519
1.9ENST000002624159ENSE00001118560chr17:41573549-4157363688DHX8_HUMAN405-434300--
1.10ENST0000026241510ENSE00001118561chr17:41576230-4157632798DHX8_HUMAN434-466330--
1.11ENST0000026241511ENSE00000731685chr17:41577324-41577471148DHX8_HUMAN467-516500--
1.12ENST0000026241512ENSE00000731684chr17:41582012-41582193182DHX8_HUMAN516-576610--
1.13ENST0000026241513ENSE00000731682chr17:41584371-41584565195DHX8_HUMAN577-641650--
1.14ENST0000026241514ENSE00000731681chr17:41584871-41585056186DHX8_HUMAN642-703620--
1.15ENST0000026241515ENSE00000731679chr17:41585177-41585387211DHX8_HUMAN704-774710--
1.16ENST0000026241516ENSE00001279910chr17:41585707-41585888182DHX8_HUMAN774-834610--
1.17ENST0000026241517ENSE00001279902chr17:41590730-41590870141DHX8_HUMAN835-881470--
1.18ENST0000026241518ENSE00001279895chr17:41594535-41594690156DHX8_HUMAN882-933520--
1.19ENST0000026241519ENSE00001279890chr17:41597498-41597635138DHX8_HUMAN934-979460--
1.20ENST0000026241520ENSE00001279884chr17:41598119-41598247129DHX8_HUMAN980-1022430--
1.21ENST0000026241521ENSE00001279875chr17:41598737-41598933197DHX8_HUMAN1023-1088660--
1.22ENST0000026241522ENSE00001279867chr17:41599415-41599594180DHX8_HUMAN1088-1148610--
1.23ENST0000026241523ENSE00001311829chr17:41600996-41601680685DHX8_HUMAN1148-1220730--

(-) 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:103
 aligned with DHX8_HUMAN | Q14562 from UniProtKB/Swiss-Prot  Length:1220

    Alignment length:130
                                   235       245       255       265       275       285       295       305       315       325       335       345       355
           DHX8_HUMAN   226 SRSQSPPKDRKDRDKYGERNLDRWRDKHVDRPPPEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSMKDVDQETGEDLNPNRRRNLV 355
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......----------..-----------------......eeeeeeeee....eeeee.......eeeehhhhh.......hhhhhh....eeeeeeeeee..eeeee..................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------S1  PDB: A:265-336 UniProt: 265-336                                     ------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: A:253-288 (gaps) UniProt: 168-288 [INCOMPLETE]  ------------------------------------------------Exon 1.8            Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------Exon 1.7  PDB: A:288-336 UniProt: 288-336        ------------------- Transcript 1 (2)
                 2eqs A 253 GSSGSS----------GE-----------------EPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSMKDVDQETGEDLNPNRRRNLV 355
                                 |   -      || -         -     | 265       275       285       295       305       315       325       335       345       355
                               258        259|               261                                                                                              
                                           260                                                                                                                

   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 2EQS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

NMR Structure(hide GO term definitions)
Chain A   (DHX8_HUMAN | Q14562)
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:0008026    ATP-dependent helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    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.
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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.
    GO:0005681    spliceosomal complex    Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

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 Related Entries

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        DHX8_HUMAN | Q145623i4u 5mqf

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