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(-) Description

Title :  STRUCTURE OF DUCK RIG-I HELICASE DOMAIN
 
Authors :  E. Kowalinski, T. Lunardi, A. A. Mccarthy, S. Cusack
Date :  28 Sep 11  (Deposition) - 19 Oct 11  (Release) - 26 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Superfamily 2 Rna Helicase, Atp And Dsrna Binding, Antiviral Signalling Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Kowalinski, T. Lunardi, A. A. Mccarthy, J. Louber, J. Brunel, B. Grigorov, D. Gerlier, S. Cusack
Structural Basis For The Activation Of Innate Immune Patter Recognition Receptor Rig-I By Viral Rna.
Cell(Cambridge, Mass. ) V. 147 423 2011
PubMed-ID: 22000019  |  Reference-DOI: 10.1016/J.CELL.2011.09.039

(-) Compounds

Molecule 1 - RETINOIC ACID INDUCIBLE PROTEIN I
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HIGH FIVE
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PFASTBAC
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: HELICASE DOMAIN, RESIDUES 242-794
    Organism Scientific: ANAS PLATYRHYNCHOS
    Organism Taxid: 8839
    Synonym: RIG-I

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4A2P)

(-) Sites  (0, 0)

(no "Site" information available for 4A2P)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A2P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4A2P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A2P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4A2P)

(-) Exons   (0, 0)

(no "Exon" information available for 4A2P)

(-) 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:479
 aligned with D3TI84_ANAPL | D3TI84 from UniProtKB/TrEMBL  Length:933

    Alignment length:548
                                   255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785        
         D3TI84_ANAPL   246 ARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSKCILVTSKTEVVENEKCNRYKEEMMNKAVEKIQKWDEETFAKKIHNLQMKERVLRD 793
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhhhhhh..eee....-----hhhhhhhhh.eeeehhhhhhhhhhh..........eeeee.hhhh...hhhhhhhhhhhhhhhh.---..eeeeee.........hhhhhhhhhhhhhhhhh..eee....hhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhhhhhh.---------....hhhhhhhhhhhhhhhhhh---hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhh..hhhhh..ee.------------------------------..eeeee.-----------.eeeee....hhhhhhhh--------..eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a2p A 246 ARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGE-----SVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNS---LPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISNLMSETEALMRTIYS---------KDFGTQNYEHWIVVTQRKCRLL---DKEEESRICRALFICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGV------------------------------NRLLIATS-----------NLVVLYEYSGNVTKMIQV--------SKCILVTSKTEVVENEKCNRYKEEMMNKAVEKIQKWDEETFAKKIHNLQMKERVLRD 793
                                   255       265       275       285       295       305       315       325    |    -|      345       355       365       375       385       395    |  405       415       425       435       445       455       465       475       485       | -       505       515        |-  |    535       545       555       565       575       585       595       605       615       625       635       645       655     |   -         -         -      |695   |     -     | 715       725  |      - |     745       755       765       775       785        
                                                                                                              330   336                                                             400 404                                                                                      493       503                  524 528                                                                                                                                  661                            692    699         711              728      737
   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 4A2P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A2P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A2P)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (D3TI84_ANAPL | D3TI84)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/TrEMBL
        D3TI84_ANAPL | D3TI84: 4a2q 4a2v 4a2w 4a2x 4a36

(-) Related Entries Specified in the PDB File

4a2q STRUCTURE OF DUCK RIG-I TANDEM CARDS AND HELICASE DOMAIN
4a2v STRUCTURE OF DUCK RIG-I C-TERMINAL DOMAIN (CTD)
4a2w STRUCTURE OF FULL-LENGTH DUCK RIG-I
4a2x STRUCTURE OF DUCK RIG-I C-TERMINAL DOMAIN (CTD) WITH 14-MER DSRNA
4a36 STRUCTURE OF DUCK RIG-I HELICASE DOMAIN BOUND TO 19 -MER DSRNA AND ATP TRANSITION STATE ANALOGUE