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(-) Description

Title :  STRUCTURE OF FULL-LENGTH DUCK RIG-I
 
Authors :  E. Kowalinski, T. Lunardi, A. A. Mccarthy, S. Cusack
Date :  29 Sep 11  (Deposition) - 19 Oct 11  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Superfamily 2 Rna Helicase, Atp And Dsrna Binding, Card, 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, B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PFASTBAC
    Expression System Strain: HIGH FIVE
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: FULL-LENGTH, RESIDUES 2-933
    Organism Common: MALLARD DUCK
    Organism Scientific: ANAS PLATYRHYNCHOS
    Organism Taxid: 8839
    Synonym: RIG-I

 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 4A2W)

(-) Sites  (0, 0)

(no "Site" information available for 4A2W)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A2W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4A2W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A2W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4A2W)

(-) Exons   (0, 0)

(no "Exon" information available for 4A2W)

(-) 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:678
 aligned with D3TI84_ANAPL | D3TI84 from UniProtKB/TrEMBL  Length:933

    Alignment length:794
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790    
         D3TI84_ANAPL     1 MTADEKRSLQCYRRYIERSLNPVYVLGNMTDWLPDELRERIRKEEERGVSGAAALFLDAVLQLEARGWFRGMLDAMLAAGYTGLAEAIENWDFSKLEKLELHRQLLKRIEATMLEVDPVALIPYISTCLIDRECEEIQQISENRSKAAGITKLIECLCRSDKEHWPKSLQLALDTTGYYRASELWDIREDNAKDVDSEMTDASEDCLEASMTYSEEAEPDDNLSENLGSAAEGIGKPPPVYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSKCILVTSKTEVVENEKCNRYKEEMMNKAVEKIQKWDEETFAKKIHNLQMKERVLRDS 794
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhh..........hhhhhhhhhhh.hhhhhh...hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhh..----------------------------------------------------------..hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh............eeee..hhhhhhhhhhhhhhhhhh....eeee...-----.hhhhhhhh.eeeehhhhhhhhhhh....hhhhh.eeeee.hhhh...hhhhhhhhhhhhhhhh......eeeeee.........hhhhhhhhhhhhhhhhh..eee....hhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhhhhh------------...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh........eeeee.hhhhhhhhhhhhhhh........ee.----------------------------...eeeee..------.....eeeee.....hhhhhh.-------...eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a2w A   1 GTADEKRSLQCYRRYIERSLNPVYVLGNMTDWLPDELRERIRKEEERGVSGAAALFLDAVLQLEARGWFRGMLDAMLAAGYTGLAEAIENWDFSKLEKLELHRQLLKRIEATMLEVDPVALIPYISTCLIDRECEEIQQISENRSKAAGITKLIECLCRSDKEHWPKSLQLALDTTGYYRASELWD----------------------------------------------------------KARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGE-----SVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISNLMSETEALMRTI------------DFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVL----------------------------DNRLLIATSV------IVQCNLVVLYEYSGNVTKMIQV-------GSKCILVTSKTEVVENEKCNRYKEEMMNKAVEKIQKWDEETFAKKIHNLQMKERVLRDS 794
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     |   -         -         -         -         -         -    |  250       260       270       280       290       300       310       320       330     | 340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490|        -   |   510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660 |       -         -         -|      700      |710       720       | -     | 740       750       760       770       780       790    
                                                                                                                                                                                                                   186                                                        245                                                                                  330   336                                                                                                                                                        491          504                                                                                                                                                           662                          691      700    707                  728     736                                                          


Chain B from PDB  Type:PROTEIN  Length:674
 aligned with D3TI84_ANAPL | D3TI84 from UniProtKB/TrEMBL  Length:933

    Alignment length:794
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790    
         D3TI84_ANAPL     1 MTADEKRSLQCYRRYIERSLNPVYVLGNMTDWLPDELRERIRKEEERGVSGAAALFLDAVLQLEARGWFRGMLDAMLAAGYTGLAEAIENWDFSKLEKLELHRQLLKRIEATMLEVDPVALIPYISTCLIDRECEEIQQISENRSKAAGITKLIECLCRSDKEHWPKSLQLALDTTGYYRASELWDIREDNAKDVDSEMTDASEDCLEASMTYSEEAEPDDNLSENLGSAAEGIGKPPPVYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSKCILVTSKTEVVENEKCNRYKEEMMNKAVEKIQKWDEETFAKKIHNLQMKERVLRDS 794
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhh..........hhhhhhhhhhh.hhhhhh...hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhh..----------------------------------------------------------..hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh............eeee..hhhhhhhhhhhhhhhhhh....eeee...-----.hhhhhhhh.eeeehhhhhhhhhhh....hhhhh.eeeee.hhhh...hhhhhhhhhhhhhhhh......eeeeee.........hhhhhhhhhhhhhhhhh..eee....hhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhhhhh------------...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhh........ee.----------------------------...eeee.---------....eeeee.....hhhhhh--------...eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a2w B   1 GTADEKRSLQCYRRYIERSLNPVYVLGNMTDWLPDELRERIRKEEERGVSGAAALFLDAVLQLEARGWFRGMLDAMLAAGYTGLAEAIENWDFSKLEKLELHRQLLKRIEATMLEVDPVALIPYISTCLIDRECEEIQQISENRSKAAGITKLIECLCRSDKEHWPKSLQLALDTTGYYRASELWD----------------------------------------------------------KARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGE-----SVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISNLMSETEALMRTI------------DFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVL----------------------------DNRLLIAT---------VQCNLVVLYEYSGNVTKMIQ--------GSKCILVTSKTEVVENEKCNRYKEEMMNKAVEKIQKWDEETFAKKIHNLQMKERVLRDS 794
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     |   -         -         -         -         -         -    |  250       260       270       280       290       300       310       320       330     | 340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490|        -   |   510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660 |       -         -         -|      | -       710       720      |  -     | 740       750       760       770       780       790    
                                                                                                                                                                                                                   186                                                        245                                                                                  330   336                                                                                                                                                        491          504                                                                                                                                                           662                          691    698       708                727      736
   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 4A2W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A2W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A2W)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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: 4a2p 4a2q 4a2v 4a2x 4a36

(-) Related Entries Specified in the PDB File

4a2p STRUCTURE OF DUCK RIG-I HELICASE DOMAIN
4a2q STRUCTURE OF DUCK RIG-I TANDEM CARDS AND HELICASE DOMAIN
4a2v STRUCTURE OF DUCK RIG-I C-TERMINAL DOMAIN (CTD)
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