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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NS1 EFFECTOR DOMAIN W182A MUTANT FROM INFLUENZA A/VIETNAM/1203/2004 (H5N1) VIRUS
 
Authors :  S. Chen, Y. B. Xiao, G. Bricogne, A. J. Sharff, R. Hilgenfeld
Date :  04 Oct 10  (Deposition) - 05 Oct 11  (Release) - 05 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.14
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E (1x),F (1x)
Biol. Unit 4:  E (1x),F (1x)
Keywords :  Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Chen, Y. B. Xiao, G. Bricogne, A. J. Sharff, R. Hilgenfeld
X-Ray Structures Of The Ns1 Effector Domain From Highly Pathogenic Influenza A/Vietnam/1203/2004 (H5N1) Virus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NONSTRUCTURAL PROTEIN 1
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P-1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL EFFECTOR DOMAIN, UNP RESIDUES 73-215
    Gene: NS1
    Mutation: YES
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 680789
    Strain: A/ENVIRONMENT/VIET NAM/1203/2004(H5N1)

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     E (1x)F (1x)
Biological Unit 4 (1x):     E (1x)F (1x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3P39)

(-) Sites  (0, 0)

(no "Site" information available for 3P39)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P39)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys D:75 -Ala D:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P39)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P39)

(-) Exons   (0, 0)

(no "Exon" information available for 3P39)

(-) 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:123
 aligned with D1LP63_9INFA | D1LP63 from UniProtKB/TrEMBL  Length:215

    Alignment length:123
                                    87        97       107       117       127       137       147       157       167       177       187       197   
         D1LP63_9INFA    78 KMPASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTGEDVKNAIGVLIGGLEWNDNTVRVTETIQRFAWRN 200
               SCOP domains d3p39a_ A: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhhhh........ee....eeeee.......eeeeeeeeee....eeeeeeeeeee....eeeeeee.......hhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p39 A  78 KMPASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTGEDVKNAIGVLIGGLEANDNTVRVTETIQRFAWRN 200
                                    87        97       107       117       127       137       147       157       167       177       187       197   


Chain B from PDB  Type:PROTEIN  Length:123
 aligned with D1LP63_9INFA | D1LP63 from UniProtKB/TrEMBL  Length:215

    Alignment length:123
                                    87        97       107       117       127       137       147       157       167       177       187       197   
         D1LP63_9INFA    78 KMPASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTGEDVKNAIGVLIGGLEWNDNTVRVTETIQRFAWRN 200
               SCOP domains d3p39b_ B: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhhhh........ee....eeeee.......eeeeeeeeee....eeeeeeeeeee....eeeeeee.......hhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p39 B  78 KMPASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTGEDVKNAIGVLIGGLEANDNTVRVTETIQRFAWRN 200
                                    87        97       107       117       127       137       147       157       167       177       187       197   


Chain C from PDB  Type:PROTEIN  Length:123
 aligned with D1LP63_9INFA | D1LP63 from UniProtKB/TrEMBL  Length:215

    Alignment length:123
                                    87        97       107       117       127       137       147       157       167       177       187       197   
         D1LP63_9INFA    78 KMPASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTGEDVKNAIGVLIGGLEWNDNTVRVTETIQRFAWRN 200
               SCOP domains d3p39c_ C: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhhhh........eeee..eeeee.......eeeeeeeeee....eeeeeeeeeee....eeeeeee.......hhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p39 C  78 KMPASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTGEDVKNAIGVLIGGLEANDNTVRVTETIQRFAWRN 200
                                    87        97       107       117       127       137       147       157       167       177       187       197   


Chain D from PDB  Type:PROTEIN  Length:126
 aligned with D1LP63_9INFA | D1LP63 from UniProtKB/TrEMBL  Length:215

    Alignment length:126
                                    84        94       104       114       124       134       144       154       164       174       184       194      
         D1LP63_9INFA    75 KALKMPASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTGEDVKNAIGVLIGGLEWNDNTVRVTETIQRFAWRN 200
               SCOP domains d3p39d_ D: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeee..hhhhhhh........ee....eeeee.......eeeeeeeeee....eeeeeeeeeee....eeeeeee.......hhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p39 D  75 KALKMPASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTGEDVKNAIGVLIGGLEANDNTVRVTETIQRFAWRN 200
                                    84        94       104       114       124       134       144       154       164       174       184       194      


Chain E from PDB  Type:PROTEIN  Length:123
 aligned with D1LP63_9INFA | D1LP63 from UniProtKB/TrEMBL  Length:215

    Alignment length:123
                                    87        97       107       117       127       137       147       157       167       177       187       197   
         D1LP63_9INFA    78 KMPASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTGEDVKNAIGVLIGGLEWNDNTVRVTETIQRFAWRN 200
               SCOP domains d3p39e_ E: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhhhh........eeee..eeeee.......eeeeeeeeee....eeeeeeeeeee....eeeeeee.......hhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p39 E  78 KMPASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTGEDVKNAIGVLIGGLEANDNTVRVTETIQRFAWRN 200
                                    87        97       107       117       127       137       147       157       167       177       187       197   


Chain F from PDB  Type:PROTEIN  Length:123
 aligned with D1LP63_9INFA | D1LP63 from UniProtKB/TrEMBL  Length:215

    Alignment length:123
                                    87        97       107       117       127       137       147       157       167       177       187       197   
         D1LP63_9INFA    78 KMPASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTGEDVKNAIGVLIGGLEWNDNTVRVTETIQRFAWRN 200
               SCOP domains d3p39f_ F: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhhhh........ee....eeeee.......eeeeeeeeee....eeeeeeeeeee....eeeeeee.......hhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p39 F  78 KMPASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTGEDVKNAIGVLIGGLEANDNTVRVTETIQRFAWRN 200
                                    87        97       107       117       127       137       147       157       167       177       187       197
   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, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P39)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3P39)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (D1LP63_9INFA | D1LP63)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0039580    suppression by virus of host PKR activity    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host PKR (protein kinase regulated by RNA) activity. Activation of PKR involves dsRNA binding followed by autophosphorylation. Phosphorylated PKR can then phosphorylate downstream targets such as the translation initiation factor eIF2 to inhibit protein synthesis. Viruses encode a number of mechanisms to inhibit the host antiviral response via PKR, including direct interaction with PKR, promoting degradation of PKR or altering the subcellular location of PKR.
    GO:0039540    suppression by virus of host RIG-I activity    Any process in which a virus stops, prevents, or reduces the activity of RIG-1 (also known as DDX58). The cytoplasmic pattern recognition RIG-I recognizes viral RNA synthesized during active viral replication and signals to protect the host against viral infection, for example by inducing the expression of antiviral cytokines.
    GO:0039657    suppression by virus of host gene expression    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. 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 (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
    GO:0039503    suppression by virus of host innate immune response    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
    GO:0039524    suppression by virus of host mRNA processing    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of mRNA processing in the host cell. mRNA processing is the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0039502    suppression by virus of host type I interferon-mediated signaling pathway    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    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:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.

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    Lys D:75 - Ala D:76   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/TrEMBL
        D1LP63_9INFA | D1LP63: 3p31 3p38

(-) Related Entries Specified in the PDB File

3p31 3p38