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(-) Description

Title :  DDX6
 
Authors :  S. Ozgur, J. Basquin, E. Conti
Date :  12 Mar 14  (Deposition) - 07 May 14  (Release) - 18 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Mathys, J. Basquin, S. Ozgur, M. Czarnocki-Cieciura, F. Bonneau, A. Aartse, A. Dziembowski, M. Nowotny, E. Conti, W. Filipowicz
Structural And Biochemical Insights To The Role Of The Ccr4-Not Complex And Ddx6 Atpase In Microrna Repression.
Mol. Cell V. 54 751 2014
PubMed-ID: 24768538  |  Reference-DOI: 10.1016/J.MOLCEL.2014.03.036

(-) Compounds

Molecule 1 - DDX6
    ChainsA, B
    EC Number3.6.4.13
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPEC_HIS_SUMO
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantSTAR PRARE
    Expression System Vector TypePLASMID
    FragmentRECA1, RECA2, RESIDUES 95-469
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymATP-DEPENDENT RNA HELICASE P54, DEAD BOX PROTEIN 6, ONCOGENE RCK

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:102 , ARG B:373 , PHE B:377 , PHE B:394BINDING SITE FOR RESIDUE ACT B1470
2AC2SOFTWAREASN A:374 , PHE A:377 , CYS B:102BINDING SITE FOR RESIDUE ACT A1470

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CT5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:144 -Gly A:145
2Thr B:144 -Gly B:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CT5)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1Q_MOTIFPS51195 DEAD-box RNA helicase Q motif profile.DDX6_HUMAN96-124
 
  2A:96-124
B:96-124
2DEAD_ATP_HELICASEPS00039 DEAD-box subfamily ATP-dependent helicases signature.DDX6_HUMAN244-252
 
  2A:244-252
B:244-252
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1Q_MOTIFPS51195 DEAD-box RNA helicase Q motif profile.DDX6_HUMAN96-124
 
  1A:96-124
-
2DEAD_ATP_HELICASEPS00039 DEAD-box subfamily ATP-dependent helicases signature.DDX6_HUMAN244-252
 
  1A:244-252
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1Q_MOTIFPS51195 DEAD-box RNA helicase Q motif profile.DDX6_HUMAN96-124
 
  1-
B:96-124
2DEAD_ATP_HELICASEPS00039 DEAD-box subfamily ATP-dependent helicases signature.DDX6_HUMAN244-252
 
  1-
B:244-252

(-) Exons   (0, 0)

(no "Exon" information available for 4CT5)

(-) Sequences/Alignments

Asymmetric 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:375
 aligned with DDX6_HUMAN | P26196 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:375
                                   104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464     
           DDX6_HUMAN    95 GNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLQKPYEINLMEELTLKGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLY 469
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.hhhhhhhhhh......hhhhhhhhhhhh....eeee......hhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhh.......eeee....hhhhhhhhh.....eeeehhhhhhhhhhhh........eeeeehhhhhh...hhhhhhhhhhh.....eeeeee...hhhhhhhhhhh....eee...........eeeeee.hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhh....eeee............eeeeee.....hhhhhhhhhh.........eeeeeehhhhhhhhhhhhhhh....ee.....hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -Q_MOTIF  PDB: A:96-124       -----------------------------------------------------------------------------------------------------------------------DEAD_ATP_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ct5 A  95 GNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLQKPYEINLMEELTLKGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLY 469
                                   104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464     

Chain B from PDB  Type:PROTEIN  Length:375
 aligned with DDX6_HUMAN | P26196 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:375
                                   104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464     
           DDX6_HUMAN    95 GNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLQKPYEINLMEELTLKGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLY 469
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.hhhhhhhhhhh.....hhhhhhhhhhhh....eeee......hhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhh.......eeee....hhhhhhhhh.....eeeehhhhhhhhhhhh........eeeeehhhhhh...hhhhhhhhhhh.....eeeeee...hhhhhhhhhhhh...eee...........eeeeee.hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhh....eeee............eeeeee.....hhhhhhhhhh.........eeeeee...hhhhhhhhhhhh....ee.....hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -Q_MOTIF  PDB: B:96-124       -----------------------------------------------------------------------------------------------------------------------DEAD_ATP_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ct5 B  95 GNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLQKPYEINLMEELTLKGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLY 469
                                   104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464     

   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 4CT5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CT5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CT5)

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DDX6_HUMAN | P26196)
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:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003724    RNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a 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: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).
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
biological process
    GO:0010501    RNA secondary structure unwinding    The process in which a secondary structure of RNA are broken or 'melted'.
    GO:0033962    cytoplasmic mRNA processing body assembly    The aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body.
    GO:0043928    exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay    The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 3'-poly(A) tail.
    GO:0045665    negative regulation of neuron differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0019827    stem cell population maintenance    The process by which an organism or tissue maintains a population of stem cells of a single type. This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types.
    GO:0019074    viral RNA genome packaging    The packaging of viral RNA (single-stranded or double-stranded) into a nucleocapsid.
cellular component
    GO:0000932    P-body    A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
    GO:0016442    RISC complex    A ribonucleoprotein complex that contains members of the Argonaute family of proteins, small interfering RNAs (siRNAs) or microRNAs (miRNAs), and miRNA or siRNA-complementary mRNAs, in addition to a number of accessory factors. The RISC complex is involved in posttranscriptional repression of gene expression through downregulation of translation or induction of mRNA degradation.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0010494    cytoplasmic stress granule    A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
    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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DDX6_HUMAN | P261961vec 2wax 2way 4crw 4ct4 5anr

(-) Related Entries Specified in the PDB File

4ct4 CNOT1 MIF4G DOMAIN - DDX6 COMPLEX