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(-) Description

Title :  P453H/I471T MUTANT OF PB2 MIDDLE DOMAIN FROM INFLUENZA VIRUS A/PUERTO RICO/8/34(H1N1) WITH M7GTP
 
Authors :  T. Tsurumura, T. Yoshida, H. Tsuge
Date :  04 Sep 13  (Deposition) - 18 Dec 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A
Keywords :  Influenza A Virus, Pb2, Middle Domain, Cap Binding, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Tsurumura, H. Qiu, T. Yoshida, Y. Tsumori, D. Hatakeyama, T. Kuzuhara, H. Tsuge
Conformational Polymorphism Of M7Gtp In Crystal Structure O The Pb2 Middle Domain From Human Influenza A Virus
Plos One V. 8 82020 2013
PubMed-ID: 24312396  |  Reference-DOI: 10.1371/JOURNAL.PONE.0082020

(-) Compounds

Molecule 1 - POLYMERASE BASIC PROTEIN 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentMIDDLE DOMAIN OF PB2, UNP RESIDUES 318-484
    GenePB2
    MutationYES
    Organism ScientificINFLUENZA A VIRUS
    Organism Taxid211044
    StrainA/PUERTO RICO/8/1934 H1N1
    SynonymRNA-DIRECTED RNA POLYMERASE SUBUNIT P3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MGT1Ligand/Ion7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:323 , ARG A:332 , LYS A:339 , ARG A:355 , HIS A:357 , GLU A:361 , PHE A:363 , LYS A:376 , PHE A:404 , LYS A:440 , HOH A:632 , HOH A:718 , HOH A:720 , HOH A:724 , HOH A:725 , HOH A:729 , HOH A:731 , HOH A:765 , HOH A:767 , HOH A:768 , HOH A:769 , HOH A:770BINDING SITE FOR RESIDUE MGT A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WI1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3WI1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WI1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WI1)

(-) Exons   (0, 0)

(no "Exon" information available for 3WI1)

(-) 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    
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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:162
 aligned with PB2_I34A1 | P03428 from UniProtKB/Swiss-Prot  Length:759

    Alignment length:162
                                   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481  
            PB2_I34A1   322 SFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGVEPIDNVMGMIGILPDMTPSIEMSMRGVRISKM 483
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee..eeeeeeee..eeeeeeee.....eeeeeeee..eeeeee...eeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhhhhhhhheee......eeee.....ee..eee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3wi1 A 322 SFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGVEHIDNVMGMIGILPDMTPSTEMSMRGVRISKM 483
                                   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481  

   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 3WI1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WI1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WI1)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PB2_I34A1 | P03428)
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: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:0019064    fusion of virus membrane with host plasma membrane    Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
    GO:0075733    intracellular transport of virus    The directed movement of a virus, or part of a virus, within the host cell.
    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:0019065    receptor-mediated endocytosis of virus by host cell    Any receptor-mediated endocytosis that is involved in the uptake of a virus into a host cell; successive instances of virus endocytosis result in the accumulation of virus particles within the cell.
    GO:0039545    suppression by virus of host MAVS activity    Any process in which a virus stops, prevents, or reduces the activity of MAVS (mitochondrial antiviral signaling protein), a signal transducer that lies downstream of the viral RNA receptors MDA-5 and RIG-I to coordinate host innate immune responses.
    GO:0039523    suppression by virus of host RNA polymerase II activity    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host RNA polymerase II activity.
    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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0019061    uncoating of virus    The process by which an incoming virus is disassembled in the host cell to release a replication-competent viral genome.
    GO:0046761    viral budding from plasma membrane    A viral budding that starts with formation of a membrane curvature in the host plasma membrane.
    GO:0019070    viral genome maturation    The processes involved in creating a mature, stable viral genome. Begins after genome replication with a newly synthesized nucleic acid and ends when the genome is ready to be packaged. Includes the addition of proteins to the newly synthesized genome, and DNA repair processes.
    GO:0019072    viral genome packaging    The encapsulation of the viral genome within the capsid.
    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:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
    GO:0019083    viral transcription    The process by which a viral genome, or part of a viral genome, is transcribed within the host cell.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0031904    endosome lumen    The volume enclosed by the membrane of an endosome.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0033650    host cell mitochondrion    A semiautonomous, self replicating organelle as found in host cells that occurs in varying numbers, shapes, and sizes in the cell cytoplasm. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PB2_I34A1 | P034282ztt 3a1g 3cw4 3wi0 4enf 4j2r 4u6o

(-) Related Entries Specified in the PDB File

3cw4 LARGE C-TERMINAL DOMAIN OF INFLUENZA A VIRUS RNA-DEPENDENT POLYMERASE PB2
3wi0