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(-) Description

Title :  STRUCTURE OF THE C-TERMINAL DOMAIN OF THE POLYMERASE COFACTOR OF RABIES VIRUS: INSIGHTS IN FUNCTION AND EVOLUTION.
 
Authors :  M. Mavrakis, A. A. Mccarthy, S. Roche, D. Blondel, R. W. H. Ruigrok
Date :  30 Apr 04  (Deposition) - 15 Oct 04  (Release) - 03 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Rabies Virus, Replication, Transcription, Polymerase, Rna-Directed Rna Polymerase, Phosphorylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Mavrakis, A. A. Mccarthy, S. Roche, D. Blondel, R. W. H. Ruigrok
Structure And Function Of The C-Terminal Domain Of The Polymerase Cofactor Of Rabies Virus
J. Mol. Biol. V. 343 819 2004
PubMed-ID: 15476803  |  Reference-DOI: 10.1016/J.JMB.2004.08.071

(-) Compounds

Molecule 1 - RNA POLYMERASE ALPHA SUBUNIT
    Chains: A
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF21
    Expression System Plasmid: ACNPVM1
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: C-TERMINAL DOMAIN, RESIDUES 186-297
    Organism Scientific: RABIES VIRUS (STRAIN CVS-11)
    Strain: CVS STRAIN
    Synonym: PHOSPHOPROTEIN, NONSTRUCTURAL PROTEIN, M1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:217 , ARG A:218 , SER A:219 , GLN A:229 , LYS A:273 , LEU A:277 , HOH A:2114 , HOH A:2115BINDING SITE FOR RESIDUE GOL A1297
2AC2SOFTWAREGLN A:229 , ASN A:270 , SER A:271 , LYS A:272 , LYS A:273 , GOL A:1300 , HOH A:2052 , HOH A:2117BINDING SITE FOR RESIDUE GOL A1298
3AC3SOFTWARESER A:196 , ARG A:218 , LYS A:231 , LEU A:276 , GOL A:1298 , HOH A:2016 , HOH A:2116 , HOH A:2117BINDING SITE FOR RESIDUE GOL A1300
4AC4SOFTWAREASP A:194 , GLU A:198 , LYS A:239 , ASP A:281 , HOH A:2055BINDING SITE FOR RESIDUE GOL A1301
5AC5SOFTWAREGLY A:246 , THR A:248 , ARG A:249 , HOH A:2118BINDING SITE FOR RESIDUE GOL A1302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VYI)

(-) Sequences/Alignments

Asymmetric/Biological 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:111
 aligned with PHOSP_RABVC | P22363 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:111
                                   195       205       215       225       235       245       255       265       275       285       295 
          PHOSP_RABVC   186 WSATNEEDDLSVEAEIAHQIAESFSKKYKFPSRSSGIFLYNFEQLKMNLDDIVKEAKNVPGVTRLAHDGSKIPLRCVLGWVALANSKKFQLLVEADKLSKIMQDDLNRYTS 296
               SCOP domains d1vyia_ A: Phosphoprotein M1, C-terminal domain                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains PP_M1-1vyiA01 A:186-296                                                                                         Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh....eeee.....eeeehhhhhh.hhhhhhhhhh...hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 1vyi A 186 WSATNEEDDLSVEAEIAHQIAESFSKKYKFPSRSSGIFLYNFEQLKMNLDDIVKEAKNVPGVTRLAHDGSKIPLRCVLGWVALANSKKFQLLVEADKLSKIMQDDLNRYTS 296
                                   195       205       215       225       235       245       255       265       275       285       295
   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, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: PP_M1] (4)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PHOSP_RABVC | P22363)
molecular function
    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: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:0075521    microtubule-dependent intracellular transport of viral material towards nucleus    The directed movement of a virus, or part of a virus, towards the host cell nucleus using host microtubules.
    GO:0039563    suppression by virus of host STAT1 activity    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host STAT1 (signal transducer and activator of transcription-1) activity. STATs are SH2 domain-containing proteins which lie downstream of many signaling receptors. Upon phosphorylation by JAKs, STAT proteins hetero- or homo-dimerize and translocate to the nucleus to activate transcription of target genes.
    GO:0039564    suppression by virus of host STAT2 activity    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host STAT2 (signal transducer and activator of transcription-2) activity. STATs are SH2 domain-containing proteins which lie downstream of many signaling receptors. Upon phosphorylation by JAKs, STAT proteins hetero- or homo-dimerize and translocate to the nucleus to activate transcription of target genes.
    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:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
    GO:0075606    transport of viral material towards nucleus    The directed movement of a virus, or part of a virus, towards the host cell nucleus. The process begins after viral entry, and ends when the viral material is at the nuclear membrane.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    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.
    GO:0019083    viral transcription    The process by which a viral genome, or part of a viral genome, is transcribed within the host cell.
cellular component
    GO:0075341    host cell PML body    A nuclear body that reacts against SP100 auto-antibodies (PML = promyelocytic leukemia) located within a cell of a host organism.
    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.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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