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(-) Description

Title :  STRUCTURE OF DUCK RIG-I HELICASE DOMAIN BOUND TO 19-MER DSRNA AND ATP TRANSITION STATE ANALOGUE
 
Authors :  E. Kowalinski, T. Lunardi, A. A. Mccarthy, S. Cusack
Date :  30 Sep 11  (Deposition) - 19 Oct 11  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.70
Chains :  Asym. Unit :  A,B,R,S,T,U
Biol. Unit 1:  A,R,S  (1x)
Biol. Unit 2:  B,T,U  (1x)
Keywords :  Rna Binding Protein-Rna Complex, 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, B
    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
 
Molecule 2 - 5'-R(*GP*CP*AP*UP*GP*CP*GP*AP*CP*CP*UP*CP*UP*GP *UP*UP*UP*GP*A)-3'
    Chains: R, T
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synonym: 19-MER
    Synthetic: YES
 
Molecule 3 - 5'-R(*UP*CP*AP*AP*AP*CP*AP*GP*AP*GP*GP*UP*CP*GP *CP*AP*UP*GP*C)-3'
    Chains: S, U
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synonym: 19-MER
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABRSTU
Biological Unit 1 (1x): A RS  
Biological Unit 2 (1x):  B  TU

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AF32Ligand/IonALUMINUM FLUORIDE
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AF31Ligand/IonALUMINUM FLUORIDE
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AF31Ligand/IonALUMINUM FLUORIDE
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (0, 0)

(no "Site" information available for 4A36)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A36)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4A36)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A36)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4A36)

(-) Exons   (0, 0)

(no "Exon" information available for 4A36)

(-) 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:523
 aligned with D3TI84_ANAPL | D3TI84 from UniProtKB/TrEMBL  Length:933

    Alignment length:550
                                   253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793
         D3TI84_ANAPL   244 KKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSKCILVTSKTEVVENEKCNRYKEEMMNKAVEKIQKWDEETFAKKIHNLQMKERVLRD 793
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh.........eeeee.hhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhh.eeeehhhhhhhhhhh....hhhhh.eeeeehhhhh...hhhhhhhhhhhhhhhhhh....eeeeee.........hhhhhhhhhhhhhhhh...eee....hhhhhhhhh...............hhhhhhhhhhhhhhhhhhhh.-------------..hhhhhhhhhhhhhhh.-------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhh........eeee....-------.hhhhhhhhhhhhhhh....eeee.hhhhh........eeeee......hhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a36 A 244 KKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISNLMSETEALMRTI-------------FGTQNYEHWIVVTQRKCR-------EEESRICRALFICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRG-------MTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSKCILVTSKTEVVENEKCNRYKEEMMNKAVEKIQKWDEETFAKKIHNLQMKERVLRD 793
                                   253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       | -         - |     513        |-      |533       543       553       563       573       583       593       603       613       623       633       643       653       663  |      -|      683       693       703       713       723       733       743       753       763       773       783       793
                                                                                                                                                                                                                                                                                 491           505              522     530                                                                                                                                     666     674                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:523
 aligned with D3TI84_ANAPL | D3TI84 from UniProtKB/TrEMBL  Length:933

    Alignment length:551
                                   252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792 
         D3TI84_ANAPL   243 TKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSKCILVTSKTEVVENEKCNRYKEEMMNKAVEKIQKWDEETFAKKIHNLQMKERVLRD 793
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhh.eeeehhhhhhhhhhh....hhhhh.eeee.hhhhh...hhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhhhhh...eee....hhhhhhhhh...............hhhhhhhhhhhhhhhhhhhh...-----------..hhhhhhhhhhhhhhh.----------..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhh........eeee....-------.hhhhhhhhhhhhhhh....eeee.hhhhh........eeeee......hhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a36 B 243 TKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISNLMSETEALMRTIYS-----------FGTQNYEHWIVVTQRKCR----------SRICRALFICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRG-------MTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSKCILVTSKTEVVENEKCNRYKEEMMNKAVEKIQKWDEETFAKKIHNLQMKERVLRD 793
                                   252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492|        -  |    512       522         -|      542       552       562       572       582       592       602       612       622       632       642       652       662   |     - |     682       692       702       712       722       732       742       752       762       772       782       792 
                                                                                                                                                                                                                                                                                    493         505              522        533                                                                                                                                  666     674                                                                                                                       


Chain R from PDB  Type:RNA  Length:19
                                                   
                 4a36 R   1 GCAUGCGACCUCUGUUUGA  19
                                    10         


Chain S from PDB  Type:RNA  Length:19
                                                   
                 4a36 S   1 UCAAACAGAGGUCGCAUGC  19
                                    10         


Chain T from PDB  Type:RNA  Length:18
                                                  
                 4a36 T   1 GCAUGCGACCUCUGUUUG  18
                                    10        


Chain U from PDB  Type:RNA  Length:18
                                                  
                 4a36 U   2 CAAACAGAGGUCGCAUGC  19
                                    11
   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 4A36)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A36)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A36)

(-) 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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  4a36
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 Related Entries

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

UniProtKB/TrEMBL
        D3TI84_ANAPL | D3TI84: 4a2p 4a2q 4a2v 4a2w 4a2x

(-) 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)
4a2w STRUCTURE OF FULL-LENGTH DUCK RIG-I
4a2x STRUCTURE OF DUCK RIG-I C-TERMINAL DOMAIN (CTD) WITH 14-MER DSRNA