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(-) Description

Title :  HUMAN DEAD-BOX RNA HELICASE DDX20, CONSERVED DOMAIN I (DEAD) IN COMPLEX WITH AMPPNP (ADENOSINE-(BETA,GAMMA)-IMIDOTRIPHOSPHATE)
 
Authors :  T. Karlberg, L. Tresaugues, C. H. Arrowsmith, H. Berglund, R. D. Busam, R. Collins, L. G. Dahlgren, A. M. Edwards, S. Flodin, A. Flores, S. Gras M. Hammarstrom, I. Johansson, A. Kallas, T. Kotenyova, L. Lehtio, M. M M. E. Nilsson, P. Nordlund, T. Nyman, C. Persson, J. Sagemark, L. Svens A. G. Thorsell, S. Van Den Berg, J. Weigelt, M. Welin, L. Holmberg-Sc Structural Genomics Consortium (Sgc)
Date :  30 Oct 07  (Deposition) - 13 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rna, Helicase, Dead, Conserved Domain I, Structural Genomics, Structural Genomics Consortium, Sgc, Atp-Binding, Dna-Binding, Hydrolase, Mrna Processing, Mrna Splicing, Nucleotide-Binding, Nucleus, Phosphorylation, Spliceosome (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Schutz, T. Karlberg, S. Van Den Berg, R. Collins, L. Lehtio, M. Hogbom, L. Holmberg-Schiavone, W. Tempel, H. W. Park, M. Hammarstrom, M. Moche, A. G. Thorsell, H. Schuler
Comparative Structural Analysis Of Human Dead-Box Rna Helicases.
Plos One V. 5 12791 2010
PubMed-ID: 20941364  |  Reference-DOI: 10.1371/JOURNAL.PONE.0012791

(-) Compounds

Molecule 1 - PROBABLE ATP-DEPENDENT RNA HELICASE DDX20
    ChainsA, B
    EC Number3.6.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC-BSA4
    Expression System StrainBL21(DE3)GOLD PRARE2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentDEAD DOMAIN
    GeneDDX20, DP103, GEMIN3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDEAD BOX PROTEIN 20, DEAD BOX PROTEIN DP 103, COMPONENT OF GEMS 3, GEMIN-3

 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
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:81 , PHE A:82 , ARG A:84 , GLN A:89 , SER A:108 , GLY A:109 , THR A:110 , GLY A:111 , LYS A:112 , THR A:113 , CYS A:114 , HOH A:385 , HOH A:399 , HOH A:408 , HOH A:467BINDING SITE FOR RESIDUE ANP A 300
2AC2SOFTWAREGLY B:81 , PHE B:82 , ARG B:84 , GLN B:89 , SER B:108 , GLY B:109 , THR B:110 , GLY B:111 , LYS B:112 , THR B:113 , CYS B:114 , HOH B:352 , HOH B:414 , HOH B:420BINDING SITE FOR RESIDUE ANP B 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B7G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3B7G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B7G)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1Q_MOTIFPS51195 DEAD-box RNA helicase Q motif profile.DDX20_HUMAN62-90
 
  2A:62-90
B:62-90
2DEAD_ATP_HELICASEPS00039 DEAD-box subfamily ATP-dependent helicases signature.DDX20_HUMAN209-217
 
  2A:209-217
B:209-217
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1Q_MOTIFPS51195 DEAD-box RNA helicase Q motif profile.DDX20_HUMAN62-90
 
  1A:62-90
-
2DEAD_ATP_HELICASEPS00039 DEAD-box subfamily ATP-dependent helicases signature.DDX20_HUMAN209-217
 
  1A:209-217
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1Q_MOTIFPS51195 DEAD-box RNA helicase Q motif profile.DDX20_HUMAN62-90
 
  1-
B:62-90
2DEAD_ATP_HELICASEPS00039 DEAD-box subfamily ATP-dependent helicases signature.DDX20_HUMAN209-217
 
  1-
B:209-217

(-) Exons   (5, 10)

Asymmetric Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003697021bENSE00001450683chr1:112297927-112298847921DDX20_HUMAN1-1011012A:62-101
B:62-101
40
40
1.2ENST000003697022ENSE00000783731chr1:112299268-11229936295DDX20_HUMAN101-132322A:101-132
B:101-132
32
32
1.3ENST000003697023ENSE00000783732chr1:112302022-112302190169DDX20_HUMAN133-189572A:133-189
B:133-189
57
57
1.4bENST000003697024bENSE00000783733chr1:112303096-112303210115DDX20_HUMAN189-227392A:189-227
B:189-227
39
39
1.5aENST000003697025aENSE00000783734chr1:112303328-112303470143DDX20_HUMAN227-275492A:227-266
B:227-266
40
40
1.5cENST000003697025cENSE00000783735chr1:112303609-112303747139DDX20_HUMAN275-321470--
1.5eENST000003697025eENSE00000783736chr1:112303848-11230390659DDX20_HUMAN321-341210--
1.5fENST000003697025fENSE00000783737chr1:112304877-11230495983DDX20_HUMAN341-368280--
1.5iENST000003697025iENSE00000783741chr1:112305299-112305404106DDX20_HUMAN369-404360--
1.5jENST000003697025jENSE00000463721chr1:112305528-112305629102DDX20_HUMAN404-438350--
1.6cENST000003697026cENSE00001142728chr1:112308359-1123106382280DDX20_HUMAN438-8243870--

(-) 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:205
 aligned with DDX20_HUMAN | Q9UHI6 from UniProtKB/Swiss-Prot  Length:824

    Alignment length:205
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261     
          DDX20_HUMAN    62 ADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRL 266
               SCOP domains d3b7ga_ A: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains 3b7gA00 A:62-266 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.hhhhhhhhhhh.....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhh.......eeee....hhhhhhhhhh...eeeehhhhhhhhhhh...hhhhh.eeeeehhhhhhh...hhhhhhhhhhhh....eeeeee...hhhhhhhhh......eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE Q_MOTIF  PDB: A:62-90        ----------------------------------------------------------------------------------------------------------------------DEAD_ATP_------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: A:62-101 UniProt: 1-101 -------------------------------Exon 1.3  PDB: A:133-189 UniProt: 133-189                -------------------------------------Exon 1.5a  PDB: A:227-266 [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.2  PDB: A:101-132        --------------------------------------------------------Exon 1.4b  PDB: A:189-227              --------------------------------------- Transcript 1 (2)
                 3b7g A  62 ADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRL 266
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261     

Chain B from PDB  Type:PROTEIN  Length:205
 aligned with DDX20_HUMAN | Q9UHI6 from UniProtKB/Swiss-Prot  Length:824

    Alignment length:205
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261     
          DDX20_HUMAN    62 ADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRL 266
               SCOP domains d3b7gb_ B: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains 3b7gB00 B:62-266 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.hhhhhhhhhhh.....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhh....eeeehhhhhhhhhhh...hhhhh.eeeeehhhhhhh...hhhhhhhhhhhh....eeeeee...hhhhhhhhh......eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE Q_MOTIF  PDB: B:62-90        ----------------------------------------------------------------------------------------------------------------------DEAD_ATP_------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: B:62-101 UniProt: 1-101 -------------------------------Exon 1.3  PDB: B:133-189 UniProt: 133-189                -------------------------------------Exon 1.5a  PDB: B:227-266 [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.2  PDB: B:101-132        --------------------------------------------------------Exon 1.4b  PDB: B:189-227              --------------------------------------- Transcript 1 (2)
                 3b7g B  62 ADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRL 266
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261     

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B7G)

(-) Gene Ontology  (36, 36)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DDX20_HUMAN | Q9UHI6)
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:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    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:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0070491    repressing transcription factor binding    Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.
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:0010501    RNA secondary structure unwinding    The process in which a secondary structure of RNA are broken or 'melted'.
    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:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0051170    nuclear import    The directed movement of substances into the nucleus.
    GO:0048477    oogenesis    The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0050810    regulation of steroid biosynthetic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    GO:0000387    spliceosomal snRNP assembly    The aggregation, arrangement and bonding together of one or more snRNA and multiple protein components to form a ribonucleoprotein complex that is involved in formation of the spliceosome.
    GO:0000244    spliceosomal tri-snRNP complex assembly    The formation of a tri-snRNP complex containing U4 and U6 (or U4atac and U6atac) snRNAs and U5 snRNAs and associated proteins. This includes reannealing of U4 and U6 (or U4atac and U6atac) snRNAs released from previous rounds of splicing to reform the U4/U6 snRNP (or U4atac/U6atac snRNP) as well as the subsequent association of the U5 snRNP with the U4/U6 snRNP (or U4atac/U6atac snRNP) to form a tri-snRNP that is ready to reassemble into another spliceosome complex.
cellular component
    GO:0097504    Gemini of coiled bodies    Nuclear bodies frequently found near or associated with Cajal bodies (also called coiled bodies or CBs). Gemini of coiled bodies, or 'gems', are similar in size and shape to CBs, and often indistinguishable under the microscope. Unlike CBs, gems do not contain small nuclear ribonucleoproteins (snRNPs); they contain a protein called survivor of motor neurons (SMN) whose function relates to snRNP biogenesis. Gems are believed to assist CBs in snRNP biogenesis, and to play a role in the etiology of spinal muscular atrophy (SMA).
    GO:0090571    RNA polymerase II transcription repressor complex    A protein complex, located in the nucleus, that possesses activity that prevents or downregulates transcription from a RNA polymerase II promoter.
    GO:0032797    SMN complex    A protein complex that contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and Unrip proteins; the complex is found in the cytoplasm and in nuclear Gems, and is involved in spliceosomal snRNP assembly in the cytoplasm and in pre-mRNA splicing in the nucleus.
    GO:0034719    SMN-Sm protein complex    A protein complex formed by the association of several methylated Sm proteins with the SMN complex; the latter contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and unrip proteins; additional proteins, including galectin-1 and galectin-3, are also found in the SMN-SM complex. The SMN-Sm complex is involved in spliceosomal snRNP assembly in the cytoplasm.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0017053    transcriptional repressor complex    A protein complex that possesses activity that prevents or downregulates transcription.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DDX20_HUMAN | Q9UHI62oxc

(-) Related Entries Specified in the PDB File

2oxc HUMAN DEAD-BOX RNA HELICASE DDX20, DEAD DOMAIN IN COMPLEX WITH ADP