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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LARGE C-TERMINAL DOMAIN OF POLYMERASE BASIC PROTEIN 2 FROM INFLUENZA VIRUS A/VIET NAM/1203/2004 (H5N1)
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  20 Oct 09  (Deposition) - 09 Mar 10  (Release) - 23 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Bird Flu, Structural Genomics, Niaid, Mrna Capping, Mrna Processing, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Yamada, M. Hatta, B. L. Staker, S. Watanabe, M. Imai, K. Shinya, Y. Sakai-Tagawa, M. Ito, M. Ozawa, T. Watanabe, S. Sakabe, C. Li, J. H. Kim, P. J. Myler, I. Phan, A. Raymond, E. Smith, R. Stacy, C. A. Nidom, S. M. Lank, R. W. Wiseman, B. N. Bimber, D. H. O'Connor, G. Neumann, L. J. Stewart, Y. Kawaoka
Biological And Structural Characterization Of A Host-Adapting Amino Acid In Influenza Virus.
Plos Pathog. V. 6 01034 2010
PubMed-ID: 20700447  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1001034

(-) Compounds

Molecule 1 - POLYMERASE PB2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28-SMT
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GenePB2
    Organism CommonA/VIET NAM/1203/2004(H5N1)
    Organism ScientificINFLUENZA A VIRUS (A/VIET NAM/1203/2004(H5N1))
    Organism Taxid284218
    StrainA/VIET NAM/1203/2004 (H5N1)
    SynonymPOLYMERASE BASIC SUBUNIT 2, POLYMERASE PROTEIN PB2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:645 , ARG A:646 , THR A:676BINDING SITE FOR RESIDUE EDO A 1
2AC2SOFTWAREHOH A:16 , HOH A:34 , HOH A:90 , ARG A:589 , GLY A:590 , ALA A:624 , PRO A:625 , THR A:662BINDING SITE FOR RESIDUE EDO A 3
3AC3SOFTWARELYS A:574 , MET A:575 , GLU A:576BINDING SITE FOR RESIDUE EDO A 4

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KC6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KC6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KC6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KC6)

(-) Exons   (0, 0)

(no "Exon" information available for 3KC6)

(-) 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:198
 aligned with Q6DNN3_9INFA | Q6DNN3 from UniProtKB/TrEMBL  Length:759

    Alignment length:200
                                   549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739
         Q6DNN3_9INFA   540 NGPESVLVNTYQWIIRNWETVKIQWSQDPTMLYNKMEFEPFQSLVPKAARGQYSGFVRTLFQQMRDVLGTFDTVQIIKLLPFAAAPPKQSRMQFSSLTVNVRGSGMRILVRGNSPVFNYNKATKRLTVLGKDAGALTEDPDEGTAGVESAVLRGFLILGKEDKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKR 739
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Flu_PB2-3kc6A01 A:540-739                                                                                                                                                                                Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..........eeee...--.eeee.......eeee....eeee..eeeee...................eeeeee.hhhhh...hhhhh.......eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kc6 A 540 NGPESVLVNTYQWIIRNWETVKIQWSQDPTMLYNKMEFEPFQSLVPKAARGQYSGFVRTLFQQMRDVLGTFDTVQIIKLLPFAAAPPKQSRMQFSSLTVNVR--GMRILVRGNSPVFNYNKATKRLTVLGKDAGALTEDPDEGTAGVESAVLRGFLILGKEDKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKR 739
                                   549       559       569       579       589       599       609       619       629       639 |  |  649       659       669       679       689       699       709       719       729       739
                                                                                                                               641  |                                                                                               
                                                                                                                                  644                                                                                               

   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 3KC6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KC6)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q6DNN3_9INFA | Q6DNN3)
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: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: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: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: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/TrEMBL
        Q6DNN3_9INFA | Q6DNN33l56 5fmm 5fmq

(-) Related Entries Specified in the PDB File

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