3D6R - JenaLib

Title :   STRUCTURE OF AN AVIAN INFLUENZA A VIRUS NS1 PROTEIN EFFECTOR DOMAIN

Authors :   B. G. Hale, W. S. Barclay, R. E. Randall, R. J. Russell

Date :   20 May 08 (Deposition) - 12 Aug 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)
Biol. Unit 2: A (2x),B (2x)
Biol. Unit 3: A (1x),B (1x)

Keywords :   Influenza, Ns1, Effector Domain, Alternative Splicing, Cytoplasm, Host-Virus Interaction, Interferon Antiviral System Evasion, Nucleus, Rna-Binding, Suppressor Of Rna Silencing, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. G. Hale, W. S. Barclay, R. E. Randall, R. J. Russell
Structure Of An Avian Influenza A Virus Ns1 Protein Effector Domain.
Virology V. 378 1 2008
PubMed-ID: 18585749 | Reference-DOI: 10.1016/J.VIROL.2008.05.026
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:114
 aligned with NS1_I76A2 | P69270 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:114
                                    98       108       118       128       138       148       158       168       178       188       198    
            NS1_I76A2    89 YITDMSIEEISREWYMLMPRQKITGGLMVKMDQAIMDKRITLKANFSVLFDQLETLVSLRAFTDDGAIVAEISPIPSMPGHSTEDVKNAIGILIGGLEWNDNSIRASENIQRFA 202
               SCOP domains d3d6ra_ A: automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee..hhhhhhh......eeeeee..eeeeee......eeeeeeeeee....eeeeeeeeeee....eeeeeee.......hhhhhhhhhhhhhhhhhhh..eeeehhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3d6r A  89 YITDMSIEEISREWYMLMPRQKITGGLMVKMDQAIMDKRITLKANFSVLFDQLETLVSLRAFTDDGAIVAEISPIPSMPGHSTEDVKNAIGILIGGLEWNDNSIRASENIQRFA 202
                                    98       108       118       128       138       148       158       168       178       188       198

Chain B from PDB  Type:PROTEIN  Length:127
 aligned with NS1_I76A2 | P69270 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:142
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222  
            NS1_I76A2    83 SSPAPRYITDMSIEEISREWYMLMPRQKITGGLMVKMDQAIMDKRITLKANFSVLFDQLETLVSLRAFTDDGAIVAEISPIPSMPGHSTEDVKNAIGILIGGLEWNDNSIRASENIQRFAWGIRDENGGPPLPPKQKRYMAR 224
               SCOP domains d3d6rb1 B:83-202 automated matches                                                                                      ---------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhhhh......eeeeee..eeeeee......eeeeeeeeeee..eeeeeeeeeeee....eeeeeee.......hhhhhhhhhhhhhhhhhh...eeeehhhhhhhh---------------....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d6r B  83 SSPAPRYITDMSIEEISREWYMLMPRQKITGGLMVKMDQAIMDKRITLKANFSVLFDQLETLVSLRAFTDDGAIVAEISPIPSMPGHSTEDVKNAIGILIGGLEWNDNSIRASENIQRFA---------------QKRYMAR 224
                                    92       102       112       122       132       142       152       162       172       182       192       202         -     | 222  
                                                                                                                                                 202             218

Legend:		→ Mismatch	(orange background)
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	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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NS1_I76A2 | P69270)

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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