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(-) Description

Title :  HUMAN DEAD-BOX RNA HELICASE DDX41, HELICASE DOMAIN
 
Authors :  T. Karlberg, D. Ogg, C. H. Arrowsmith, H. Berglund, R. D. Busam, R. Colli L. G. Dahlgren, A. Edwards, S. Flodin, A. Flores, S. Graslund, B. M. Hal M. Hammarstrom, I. Johansson, T. Kotenyova, L. Lehtio, M. Moche, P. No T. Nyman, C. Persson, J. Sagemark, P. Stenmark, M. Sundstrom, A. G. Tho S. Van Den Berg, J. Weigelt, L. Holmberg-Schiavone, Structural Ge Consortium (Sgc)
Date :  19 Mar 07  (Deposition) - 03 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rna, Helicase, Dead, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase (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 - ATP-DEPENDENT RNA HELICASE DDX41
    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
    FragmentHELICASE DOMAIN
    GeneDDX41, ABS
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDEAD BOX PROTEIN 41, DEAD BOX PROTEIN ABSTRAKT HOMOLOG

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2P6N)

(-) Sites  (0, 0)

(no "Site" information available for 2P6N)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P6N)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:433 -Pro A:434
2Pro B:433 -Pro B:434

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076362R525HDDX41_HUMANDisease (MPLPF)869312828A/BC525H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076362R525HDDX41_HUMANDisease (MPLPF)869312828AC525H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076362R525HDDX41_HUMANDisease (MPLPF)869312828BC525H

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P6N)

(-) Exons   (0, 0)

(no "Exon" information available for 2P6N)

(-) 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:160
 aligned with DDX41_HUMAN | Q9UJV9 from UniProtKB/Swiss-Prot  Length:622

    Alignment length:163
                                   415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565   
          DDX41_HUMAN   406 LDVIQEVEYVKEEAKMVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGRSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQVLHC 568
               SCOP domains d2p6na_ A: automated matches                                                                                                                                        SCOP domains
               CATH domains 2p6nA00 A:406-568 P-loop containing nucleotide triphosphate hydrolases                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.hhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh...eeeehhhhhh........eeee.....hhhhhhhhhh....---..eeeeee....hhhhhhhhhhhhhhh....hhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------H------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p6n A 406 LDVIQEVEYVKEEAKMVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGC---TGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQVLHC 568
                                   415       425       435       445       455       465       475       485       495       505       515       525   |   535       545       555       565   
                                                                                                                                                 525 529                                       

Chain B from PDB  Type:PROTEIN  Length:158
 aligned with DDX41_HUMAN | Q9UJV9 from UniProtKB/Swiss-Prot  Length:622

    Alignment length:160
                                   415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565
          DDX41_HUMAN   406 LDVIQEVEYVKEEAKMVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGRSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQV 565
               SCOP domains d2p6nb_ B: automated matches                                                                                                                                     SCOP domains
               CATH domains 2p6nB00 B:406-565 P-loop containing nucleotide triphosphate hydrolases                                                                                           CATH domains
           Pfam domains (1) --------------------------------------------Helicase_C-2p6nB01 B:450-526                                                 --------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------Helicase_C-2p6nB02 B:450-526                                                 --------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeeee.hhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh....eeeehhhhhh........eeee.....hhhhhhhhhh.....--.eeeeeee....hhhhhhhhhhhhhhh....hhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------H---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p6n B 406 LDVIQEVEYVKEEAKMVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCS--TGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQV 565
                                   415       425       435       445       455       465       475       485       495       505       515       525|  |   535       545       555       565
                                                                                                                                                  526  |                                    
                                                                                                                                                     529                                    

   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  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DDX41_HUMAN | Q9UJV9)
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:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0035458    cellular response to interferon-beta    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-beta stimulus. Interferon-beta is a type I interferon.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    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.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0032481    positive regulation of type I interferon production    Any process that activates or increases the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0032479    regulation of type I interferon production    Any process that modulates the frequency, rate, or extent of interferon type I production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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

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

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        DDX41_HUMAN | Q9UJV95gvr 5gvs 5h1y

(-) Related Entries Specified in the PDB File

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