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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PUTATIVE CAP-BINDING DOMAIN OF THE PB2 SUBUNIT OF THOGOTO VIRUS POLYMERASE (FORM 2)
 
Authors :  D. Guilligay, J. Kadlec, T. Crepin, T. Lunardi, D. Bouvier, G. Kochs, R. W. H. Ruigrok, S. Cusack
Date :  01 Dec 13  (Deposition) - 05 Feb 14  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Guilligay, J. Kadlec, T. Crepin, T. Lunardi, D. Bouvier, G. Kochs, R. W. H. Ruigrok, S. Cusack
Comparative Structural And Functional Analysis Of Orthomyxovirus Polymerase Cap-Snatching Domains.
Plos One V. 9 84973 2014
PubMed-ID: 24454773  |  Reference-DOI: 10.1371/JOURNAL.PONE.0084973

(-) Compounds

Molecule 1 - POLYMERASE BASIC PROTEIN 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: CODON PLUS-RIL
    Expression System Vector: PPROEXHTB
    Expression System Vector Type: PLASMID
    Fragment: PUTATIVE CAP-BINDING DOMAIN, RESIDUES 323-486
    Organism Scientific: THOGOTO VIRUS
    Organism Taxid: 11569
    Synonym: RNA-DIRECTED RNA POLYMERASE SUBUNIT P3

 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 4CHF)

(-) Sites  (0, 0)

(no "Site" information available for 4CHF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:418 -Pro A:419
2Glu B:418 -Pro B:419

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4CHF)

(-) 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:161
 aligned with PB2_THOGV | Q9YNA4 from UniProtKB/Swiss-Prot  Length:769

    Alignment length:161
                                   334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484 
            PB2_THOGV   325 HHTMKIRSTKFSILNSDHPRIEVKKVFSLSPDVQVTIPYRRFKGKAKVYFQNDQIQGYFSCTDRQIDEIKISAPKNAPLLEPLLDICYYGSFIEPGFEQTFGFYPAGKREFVDSFFMHHSKDHKAFLIHMGLDKDLSLPLSPELNWKEPALSKVCRVTELD 485
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eeeeeeee....eee..eeeee..eeee..eee...eeeeeeee..eeeeeeee..eeeeeeee......hhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhee...................ee..eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4chf A 325 HHTMKIRSTKFSILNSDHPRIEVKKVFSLSPDVQVTIPYRRFKGKAKVYFQNDQIQGYFSCTDRQIDEIKISAPKNAPLLEPLLDICYYGSFIEPGFEQTFGFYPAGKREFVDSFFMHHSKDHKAFLIHMGLDKDLSLPLSPELNWKEPALSKVCRVTELD 485
                                   334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484 


Chain B from PDB  Type:PROTEIN  Length:160
 aligned with PB2_THOGV | Q9YNA4 from UniProtKB/Swiss-Prot  Length:769

    Alignment length:160
                                   335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485
            PB2_THOGV   326 HTMKIRSTKFSILNSDHPRIEVKKVFSLSPDVQVTIPYRRFKGKAKVYFQNDQIQGYFSCTDRQIDEIKISAPKNAPLLEPLLDICYYGSFIEPGFEQTFGFYPAGKREFVDSFFMHHSKDHKAFLIHMGLDKDLSLPLSPELNWKEPALSKVCRVTELD 485
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eeeeeeee....eee..eeeee..eeee..eee...eeeeeeee..eeeeeeee..eeeeeeee......hhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhee...................ee..eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4chf B 326 HTMKIRSTKFSILNSDHPRIEVKKVFSLSPDVQVTIPYRRFKGKAKVYFQNDQIQGYFSCTDRQIDEIKISAPKNAPLLEPLLDICYYGSFIEPGFEQTFGFYPAGKREFVDSFFMHHSKDHKAFLIHMGLDKDLSLPLSPELNWKEPALSKVCRVTELD 485
                                   335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485
   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 4CHF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PB2_THOGV | Q9YNA4)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003968    RNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
biological process
    GO:0006370    7-methylguanosine mRNA capping    Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript.
    GO:0075526    cap snatching    A transcription initiation process during which a nucleotide sequence between 10 and 20 nucleotides in size is cleaved from the 5' end of host mRNAs by a viral RNA-dependent polymerase. The capped leader sequence obtained is subsequently used to prime transcription on the viral genome, which ultimately leads to the synthesis of capped, translatable viral mRNAs.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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    Glu A:418 - Pro A:419   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        PB2_THOGV | Q9YNA4: 4chd 4che

(-) Related Entries Specified in the PDB File

4cgs CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF THE PA SUBUNIT OF DHORI VIRUS POLYMERASE
4cgx CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF THE PA SUBUNIT OF THOGOTO VIRUS POLYMERASE (FORM 1)
4chc CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF THE PA SUBUNIT OF THOGOTO VIRUS POLYMERASE (FORM 2)
4chd CRYSTAL STRUCTURE OF THE '627' DOMAIN OF THE PB2 SUBUNIT OF THOGOTO VIRUS POLYMERASE
4che CRYSTAL STRUCTURE OF THE PUTATIVE CAP-BINDING DOMAIN OF THE PB2 SUBUNIT OF THOGOTO VIRUS POLYMERASE