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(-) Description

Title :  CRYSTAL TRUCTURE OF RNA BINDING DOMAIN OF INFLUENZA B VIRUS NON-STRUCTURAL PROTEIN
 
Authors :  J. A. Khan, C. Yin, R. M. Krug, G. T. Montelione, L. Tong, Northeast Stru Genomics Consortium (Nesg)
Date :  11 Sep 04  (Deposition) - 20 Sep 05  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Influenza B Virus, Rna Binding Domain, Non-Structural Protein, Ns1B, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Yin, J. A. Khan, G. V. Swapna, A. Ertekin, R. M. Krug, L. Tong, G. T. Montelione
Conserved Surface Features Form The Double-Stranded Rna Binding Site Of Non-Structural Protein 1 (Ns1) From Influenza A And B Viruses.
J. Biol. Chem. V. 282 20584 2007
PubMed-ID: 17475623  |  Reference-DOI: 10.1074/JBC.M611619200

(-) Compounds

Molecule 1 - NONSTRUCTURAL PROTEIN NS1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET-15B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: 8
    Organism Scientific: INFLUENZA B VIRUS (B/LEE/40)
    Organism Taxid: 107412
    Strain: B/LEE/40

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 19)

Asymmetric Unit (1, 19)
No.NameCountTypeFull Name
1BR19Ligand/IonBROMIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU B:32 , LYS B:52BINDING SITE FOR RESIDUE BR B 301
02AC2SOFTWAREGLY B:13 , GLY B:15BINDING SITE FOR RESIDUE BR B 302
03AC3SOFTWAREARG B:33BINDING SITE FOR RESIDUE BR B 303
04AC4SOFTWAREASP A:92 , HOH A:436BINDING SITE FOR RESIDUE BR A 304
05AC5SOFTWAREARG A:33 , HOH A:375BINDING SITE FOR RESIDUE BR A 305
06AC6SOFTWARELYS A:83 , ALA A:95BINDING SITE FOR RESIDUE BR A 306
07AC7SOFTWAREARG A:38 , GLU B:11BINDING SITE FOR RESIDUE BR A 308
08AC8SOFTWAREGLY A:99 , ALA B:19 , ASN B:22BINDING SITE FOR RESIDUE BR B 309
09AC9SOFTWAREGLN A:37 , GLY A:96 , ILE A:97 , ASP B:92BINDING SITE FOR RESIDUE BR A 310
10BC1SOFTWAREARG A:33 , LYS A:86 , GLY A:96 , HOH A:364 , LEU B:89BINDING SITE FOR RESIDUE BR A 311
11BC2SOFTWARELYS A:83BINDING SITE FOR RESIDUE BR A 312
12BC3SOFTWAREGLU A:101 , PRO A:102 , TYR A:103BINDING SITE FOR RESIDUE BR A 313
13BC4SOFTWARETYR A:31 , ARG A:47 , ARG B:47BINDING SITE FOR RESIDUE BR A 314
14BC5SOFTWAREARG A:47BINDING SITE FOR RESIDUE BR A 315
15BC6SOFTWAREASN A:22 , MET A:84BINDING SITE FOR RESIDUE BR A 316
16BC7SOFTWARESER B:35 , TRP B:36 , HIS B:49BINDING SITE FOR RESIDUE BR B 317
17BC8SOFTWARETYR A:42 , PRO A:43 , HOH B:334BINDING SITE FOR RESIDUE BR A 318
18BC9SOFTWAREMET B:72 , SER B:73BINDING SITE FOR RESIDUE BR B 319
19CC1SOFTWARESER B:73 , LEU B:74 , GLU B:75BINDING SITE FOR RESIDUE BR B 320

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XEQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XEQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XEQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XEQ)

(-) Exons   (0, 0)

(no "Exon" information available for 1XEQ)

(-) 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:89
 aligned with NS1_INBLE | P03502 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:89
                                    24        34        44        54        64        74        84        94         
            NS1_INBLE    15 GATNATINFEAGILECYERFSWQRALDYPGQDRLHRLKRKLESRIKTHNKSEPENKRMSLEERKAIGVKMMKVLLFMDPSAGIEGFEPY 103
               SCOP domains d1xeqa1 A:15-103 N-terminal, RNA-binding domain of nonstructural protein NS1              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 1xeq A  15 GATNATINFEAGILECYERFSWQRALDYPGQDRLHRLKRKLESRIKTHNKSEPENKRMSLEERKAIGVKMMKVLLFMDPSAGIEGFEPY 103
                                    24        34        44        54        64        74        84        94         


Chain B from PDB  Type:PROTEIN  Length:85
 aligned with NS1_INBLE | P03502 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:85
                                    18        28        38        48        58        68        78        88     
            NS1_INBLE     9 QIEVGPGATNATINFEAGILECYERFSWQRALDYPGQDRLHRLKRKLESRIKTHNKSEPENKRMSLEERKAIGVKMMKVLLFMDP  93
               SCOP domains d1xeqb_ B: N-terminal, RNA-binding domain of nonstructural protein NS1                SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Flu_B_NS1-1xeqB01 B:9-93                                                              Pfam domains (1)
           Pfam domains (2) Flu_B_NS1-1xeqB02 B:9-93                                                              Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 1xeq B   9 QIEVGPGATNATINFEAGILECYERFSWQRALDYPGQDRLHRLKRKLESRIKTHNKSEPENKRMSLEERKAIGVKMMKVLLFMDP  93
                                    18        28        38        48        58        68        78        88
   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, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1XEQ)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Flu_B_NS1] (2)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NS1_INBLE | P03502)
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:0039579    suppression by virus of host ISG15 activity    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host ubiquitin-like protein ISG15 activity. ISG15 is a ubiquitin-like protein that is conjugated to lysine residues on various target proteins. Viruses escape from the antiviral activity of ISG15 by using different mechanisms; the influenza B virus NS1 protein for instance blocks the covalent linkage of ISG15 to its target proteins by directly interacting with ISG15. The papain-like protease from the coronavirus cleaves ISG15 derivatives.
    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: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: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.

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 Related Entries

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

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        NS1_INBLE | P03502: 3r66 3rt3 3sdl

(-) Related Entries Specified in the PDB File

1ns1 RELATED ID: OR2 RELATED DB: TARGETDB