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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN RIG-I CTD BOUND TO A 14-BP BLUNT-ENDED DSRNA
 
Authors :  P. Li
Date :  16 Aug 10  (Deposition) - 03 Nov 10  (Release) - 23 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Innate Immunity, Viral Rna Sensing, Rna Binding Domain, Ips-1, Cytosolic, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Lu, C. T. Ranjith-Kumar, L. Hao, C. C. Kao, P. Li
Crystal Structure Of Rig-I C-Terminal Domain Bound To Blunt-Ended Double-Strand Rna Without 5' Triphosphate.
Nucleic Acids Res. V. 39 1565 2011
PubMed-ID: 20961956  |  Reference-DOI: 10.1093/NAR/GKQ974

(-) Compounds

Molecule 1 - ATP-DEPENDENT RNA HELICASE DDX58
    Chains: A, B
    EC Number: 3.6.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Fragment: C-TERMINAL DOMAIN
    Gene: DDX58
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DEAD BOX PROTEIN 58, RETINOIC ACID-INDUCIBLE GENE 1 PROTEIN, RIG-1, RETINOIC ACID-INDUCIBLE GENE I PROTEIN, RIG-I
 
Molecule 2 - RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
    Chains: C, D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:810 , CYS A:813 , CYS A:864 , CYS A:869BINDING SITE FOR RESIDUE ZN A 2
2AC2SOFTWARECYS B:810 , CYS B:813 , CYS B:864 , CYS B:869BINDING SITE FOR RESIDUE ZN B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OG8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OG8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OG8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OG8)

(-) Exons   (2, 4)

Asymmetric/Biological Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003798831aENSE00000928042chr9:32526322-32526059264DDX58_HUMAN1-36360--
1.2ENST000003798832ENSE00001788537chr9:32500937-32500803135DDX58_HUMAN36-81460--
1.3ENST000003798833ENSE00001679623chr9:32493940-32493759182DDX58_HUMAN81-141610--
1.4ENST000003798834ENSE00000695271chr9:32492536-32492389148DDX58_HUMAN142-191500--
1.5ENST000003798835ENSE00001797315chr9:32491418-32491299120DDX58_HUMAN191-231410--
1.6ENST000003798836ENSE00000695265chr9:32489449-32489342108DDX58_HUMAN231-267370--
1.7ENST000003798837ENSE00000695262chr9:32488885-32488732154DDX58_HUMAN267-318520--
1.8ENST000003798838ENSE00000695259chr9:32488201-32487943259DDX58_HUMAN318-404870--
1.9ENST000003798839ENSE00000695256chr9:32487631-32487469163DDX58_HUMAN405-459550--
1.10ENST0000037988310ENSE00000695252chr9:32485277-32485173105DDX58_HUMAN459-494360--
1.11ENST0000037988311ENSE00000695248chr9:32481495-32481338158DDX58_HUMAN494-546530--
1.12ENST0000037988312ENSE00000928040chr9:32480352-32480217136DDX58_HUMAN547-592460--
1.13ENST0000037988313ENSE00000982630chr9:32477129-32476981149DDX58_HUMAN592-641500--
1.14ENST0000037988314ENSE00000982631chr9:32473063-3247297391DDX58_HUMAN642-672310--
1.15ENST0000037988315ENSE00000982632chr9:32467930-32467760171DDX58_HUMAN672-729580--
1.16ENST0000037988316ENSE00000982633chr9:32466439-32466288152DDX58_HUMAN729-779510--
1.17ENST0000037988317ENSE00001091722chr9:32459512-32459369144DDX58_HUMAN780-827482A:803-827
B:801-827		25
27
1.18aENST0000037988318aENSE00001247665chr9:32457416-324557031714DDX58_HUMAN828-925982A:828-925
B:828-925		98
98

(-) Sequences/Alignments

Asymmetric/Biological 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:126
 aligned with DDX58_HUMAN | O95786 from UniProtKB/Swiss-Prot  Length:925

    Alignment length:126
                                                                                                                                                    925   
                                   812       822       832       842       852       862       872       882       892       902       912       922  |   
          DDX58_HUMAN   803 KENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEMSK---   -
               SCOP domains d3og8a_ A: RIG-I C-terminal domain                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee.....eeee...eeee...eeee...hhhh.eeeee.....ee..ee..eeeee.......eeeeeeee..eeeeee....eeeee.....ee...hhhhh.......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.17  PDB: A:803-827Exon 1.18a  PDB: A:828-925 UniProt: 828-925                                                       --- Transcript 1
                 3og8 A 803 KENKKLLCRKCKALACYTADVRVIEESHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEMSKLEH 928
                                   812       822       832       842       852       862       872       882       892       902       912       922      


Chain B from PDB  Type:PROTEIN  Length:128
 aligned with DDX58_HUMAN | O95786 from UniProtKB/Swiss-Prot  Length:925

    Alignment length:128
                                                                                                                                                      925   
                                   810       820       830       840       850       860       870       880       890       900       910       920    |   
          DDX58_HUMAN   801 PDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEMSK---   -
               SCOP domains d3og8b_ B: RIG-I C-terminal domain                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---RIG-I_C-RD-3og8B01 B:804-925                                                                                              --- Pfam domains (1)
           Pfam domains (2) ---RIG-I_C-RD-3og8B02 B:804-925                                                                                              --- Pfam domains (2)
         Sec.struct. author .....eeeee.....eeee...eeee...eeee.hhhhhh.eeee......ee..eeeeeeeee.......eeeeeeee..eeeeee....eeeee.....ee...hhhhh....ee.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.17  PDB: B:801-827  Exon 1.18a  PDB: B:828-925 UniProt: 828-925                                                       --- Transcript 1
                 3og8 B 801 MDKENKKLLCRKCKALACYTADVRVIEESHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEMSKLEH 928
                                   810       820       830       840       850       860       870       880       890       900       910       920        


Chain C from PDB  Type:RNA  Length:14
                                              
                 3og8 C   1 GGCGCGCGCGCGCC  14
                                    10    


Chain D from PDB  Type:RNA  Length:14
                                              
                 3og8 D   1 GGCGCGCGCGCGCC  14
                                    10
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OG8)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: RIG-I_C-RD] (10)

(-) Gene Ontology  (46, 46)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DDX58_HUMAN | O95786)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    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:0016817    hydrolase activity, acting on acid anhydrides    Catalysis of the hydrolysis of any acid anhydride.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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).
    GO:0003727    single-stranded RNA binding    Interacting selectively and non-covalently with single-stranded RNA.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0039529    RIG-I signaling pathway    Any series of molecular signals generated as a consequence of the cytoplasmic pattern recognition receptor (PRR) RIG-1 (also known as DDX58) binding to viral RNA. RIG-I detects RNA synthesized during active viral replication and triggers a signaling pathway to protect the host against viral infection, for example by inducing the expression of antiviral cytokines.
    GO:0039528    cytoplasmic pattern recognition receptor signaling pathway in response to virus    Any series of molecular signals generated as a consequence of a virus or viral RNA binding to a pattern recognition receptor (PRR) located in the cytoplasm. Cytosolic PRRs such as RIG-I (DDX58) and MDA-5 (IFIH1) detect RNA synthesized during active viral replication and trigger a signaling pathway to protect the host against viral infection, for example by inducing the expression of antiviral cytokines.
    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:0009597    detection of virus    The series of events in which a stimulus from a virus is received and converted into a molecular signal.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0032480    negative regulation of type I interferon production    Any process that stops, prevents, or reduces 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:0002230    positive regulation of defense response to virus by host    Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0032725    positive regulation of granulocyte macrophage colony-stimulating factor production    Any process that activates or increases the frequency, rate, or extent of granulocyte macrophage colony-stimulating factor production.
    GO:0032727    positive regulation of interferon-alpha production    Any process that activates or increases the frequency, rate, or extent of interferon-alpha production.
    GO:0032728    positive regulation of interferon-beta production    Any process that activates or increases the frequency, rate, or extent of interferon-beta production.
    GO:0032755    positive regulation of interleukin-6 production    Any process that activates or increases the frequency, rate, or extent of interleukin-6 production.
    GO:0032757    positive regulation of interleukin-8 production    Any process that activates or increases the frequency, rate, or extent of interleukin-8 production.
    GO:0051091    positive regulation of sequence-specific DNA binding transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0042993    positive regulation of transcription factor import into nucleus    Any process that activates or increases the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus.
    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:0030334    regulation of cell migration    Any process that modulates the frequency, rate or extent of cell migration.
    GO:0034344    regulation of type III interferon production    Any process that modulates the frequency, rate, or extent of type III interferon production. Interferon lambda is the only member of the type III interferon found so far.
    GO:0043330    response to exogenous dsRNA    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 exogenous double-stranded RNA stimulus.
    GO:0009615    response to virus    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 stimulus from a virus.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005923    bicellular tight junction    An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.

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  DDX58_HUMAN | O95786
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 Related Entries

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

UniProtKB/Swiss-Prot
        DDX58_HUMAN | O95786: 2lwd 2lwe 2qfb 2qfd 2rmj 2ykg 3lrn 3lrr 3ncu 3zd6 3zd7 4ay2 4bpb 4nqk 4on9 4p4h 5e3h 5f98 5f9f 5f9h

(-) Related Entries Specified in the PDB File

3lrn RIG-I CTD BOUND TO A 14-BP 5' PPP DSRNA WITH THE SAME SEQUENCE AS THIS ENTRY
3lrr RIG-I CTD BOUND TO A 12-BP 5' PPP DSRNA