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(-) Description

Title :  CRYSTAL STRUCTURE OF RNA POLYMERASE PB1-PB2 SUBUNITS FROM INFLUENZA A VIRUS
 
Authors :  K. Sugiyama, E. Obayashi, S. -Y. Park
Date :  08 Oct 08  (Deposition) - 09 Jun 09  (Release) - 07 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Influenza Virus, Rna Polymerase, Pb1-Pb2 Complex Form, Nucleotide-Binding, Nucleotidyltransferase, Nucleus, Rna Replication, Rna-Directed Rna Polymerase, Transferase, Mitochondrion, Mrna Capping, Mrna Processing, Virion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Sugiyama, E. Obayashi, A. Kawaguchi, Y. Suzuki, J. R. H. Tame, K. Nagata, S. -Y. Park
Structural Insight Into The Essential Pb1-Pb2 Subunit Contact Of The Influenza Virus Rna Polymerase
Embo J. V. 28 1803 2009
PubMed-ID: 19461581  |  Reference-DOI: 10.1038/EMBOJ.2009.138
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA-DIRECTED RNA POLYMERASE CATALYTIC SUBUNIT
    Chains: A, C
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET28B
    Expression System Strain: B824(DE3)CODONPLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PB1 C-TERMINAL FRAGMENT, UNP RESIDUES 679-757
    Gene: PB1
    Organism Scientific: INFLUENZA A VIRUS (A/PUERTO RICO/8/34(H1N1))
    Organism Taxid: 211044
    Synonym: RNA POLYMERASE PB1 SUBUNIT, POLYMERASE BASIC PROTEIN 1, PB1, RNA-DIRECTED RNA POLYMERASE SUBUNIT P1
 
Molecule 2 - POLYMERASE BASIC PROTEIN 2
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET28B
    Expression System Strain: B834(DE3)CODONPLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PB2 N-TERMINAL RAGMENT, UNP RESIDUES 1-37
    Gene: PB2
    Organism Scientific: INFLUENZA A VIRUS (A/PUERTO RICO/8/34(H1N1))
    Organism Taxid: 211044
    Synonym: RNA POLYMERASE PB2 SUBUNIT, RNA-DIRECTED RNA POLYMERASE SUBUNIT P3

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric Unit (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2ZTT)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZTT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZTT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZTT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZTT)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZTT)

(-) 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:73
 aligned with RDRP_I34A1 | P03431 from UniProtKB/Swiss-Prot  Length:757

    Alignment length:73
                                   694       704       714       724       734       744       754   
           RDRP_I34A1   685 DEQMYQRCCNLFEKFFPSSSYRRPVGISSMVEAMVSRARIDARIDFESGRIKKEEFTEIMKICSTIEELRRQK 757
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 2ztt A 685 DEQmYQRCCNLFEKFFPSSSYRRPVGISSmVEAmVSRARIDARIDFESGRIKKEEFTEImKICSTIEELRRQK 757
                               |   694       704       714   |   724       734       744       754   
                             688-MSE                   714-MSE                       744-MSE         
                                                           718-MSE                                   


Chain B from PDB  Type:PROTEIN  Length:37
 aligned with PB2_I34A1 | P03428 from UniProtKB/Swiss-Prot  Length:759

    Alignment length:37
                              1                                  
                              |      8        18        28       
            PB2_I34A1     - --MERIKELRNLMSQSRTREILTKTTVDHMAIIKKYT  35
               SCOP domains ------------------------------------- SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                 2ztt B  -1 GSmERIKELRNLmSQSRTREILTKTTVDHmAIIKKYT  35
                              |      8  |     18        28       
                              |        11-MSE           28-MSE   
                              1-MSE                              


Chain C from PDB  Type:PROTEIN  Length:71
 aligned with RDRP_I34A1 | P03431 from UniProtKB/Swiss-Prot  Length:757

    Alignment length:71
                                   693       703       713       723       733       743       753 
           RDRP_I34A1   684 EDEQMYQRCCNLFEKFFPSSSYRRPVGISSMVEAMVSRARIDARIDFESGRIKKEEFTEIMKICSTIEELR 754
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
           Pfam domains (1) Flu_PB1-2zttC01 C:684-742                                  ------------ Pfam domains (1)
           Pfam domains (2) Flu_PB1-2zttC02 C:684-742                                  ------------ Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 2ztt C 684 EDEQmYQRCCNLFEKFFPSSSYRRPVGISSmVEAmVSRARIDARIDFESGRIKKEEFTEImKICSTIEELR 754
                                |  693       703       713|   |  723       733       743|      753 
                              688-MSE                   714-MSE                       744-MSE      
                                                            718-MSE                                


Chain D from PDB  Type:PROTEIN  Length:37
 aligned with PB2_I34A1 | P03428 from UniProtKB/Swiss-Prot  Length:759

    Alignment length:37
                              1                                  
                              |      8        18        28       
            PB2_I34A1     - --MERIKELRNLMSQSRTREILTKTTVDHMAIIKKYT  35
               SCOP domains ------------------------------------- SCOP domains
               CATH domains ------------------------------------- CATH domains
           Pfam domains (1) --Flu_PB2-2zttD01 D:1-35              Pfam domains (1)
           Pfam domains (2) --Flu_PB2-2zttD02 D:1-35              Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                 2ztt D  -1 GSmERIKELRNLmSQSRTREILTKTTVDHmAIIKKYT  35
                              |      8  |     18        28       
                              1-MSE    11-MSE           28-MSE
   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 2ZTT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZTT)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: Flu_PB1] (2)
(-)
Clan: no clan defined [family: Flu_PB2] (8)

(-) Gene Ontology  (35, 55)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (RDRP_I34A1 | P03431)
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.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    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: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: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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
    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:0039694    viral RNA genome replication    The replication of a viral RNA 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: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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

Chain B,D   (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 | P03428: 3a1g 3cw4 3wi0 3wi1 4enf 4j2r 4u6o
        RDRP_I34A1 | P03431: 2znl 3a1g

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2ZTT)