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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LARGE C-TERMINAL DOMAIN OF POLYMERASE BASIC PROTEIN 2 FROM INFLUENZA VIRUS A/MEXICO/INDRE4487/2009(H1N1)
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  31 Oct 09  (Deposition) - 09 Mar 10  (Release) - 23 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Pb2 C-Terminal Domain, Swine Flu, H1N1, 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, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-SMT
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL DOMAIN
    GenePB2
    Organism ScientificINFLUENZA A VIRUS (A/MEXICO/INDRE4487/2009(H1N1))
    Organism Taxid643780
    StrainA/MEXICO/INDRE4487/2009(H1N1)

 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  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:14 , HOH A:187 , MET A:603 , VAL A:606 , LEU A:607 , GLY A:608 , THR A:609 , PHE A:610BINDING SITE FOR RESIDUE GOL A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KHW)

(-) 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:201
 aligned with C3W6M3_I09A3 | C3W6M3 from UniProtKB/TrEMBL  Length:759

    Alignment length:201
                                   550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740 
         C3W6M3_I09A3   541 GPESVLVNTYQWIIRNWEIVKIQWSQDPTMLYNKMEFEPFQSLVPKATRSRYSGFVRTLFQQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGLRILVRGNSPVFNYNKATKRLTVLGKDAGALTEDPDEGTSGVESAVLRGFLILGKEDKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRDS 741
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..........eeeee....eeeee.......eee.....eeee..eeeee...................eeeeee.hhhhh..ee.hhh.......eeeeeee..eeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3khw A 541 GPESVLVNTYQWIIRNWEIVKIQWSQDPTMLYNKMEFEPFQSLVPKATRSRYSGFVRTLFQQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGLRILVRGNSPVFNYNKATKRLTVLGKDAGALTEDPDEGTSGVESAVLRGFLILGKEDKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRDS 741
                                   550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740 

Chain B from PDB  Type:PROTEIN  Length:201
 aligned with C3W6M3_I09A3 | C3W6M3 from UniProtKB/TrEMBL  Length:759

    Alignment length:201
                                   550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740 
         C3W6M3_I09A3   541 GPESVLVNTYQWIIRNWEIVKIQWSQDPTMLYNKMEFEPFQSLVPKATRSRYSGFVRTLFQQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGLRILVRGNSPVFNYNKATKRLTVLGKDAGALTEDPDEGTSGVESAVLRGFLILGKEDKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRDS 741
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Flu_PB2-3khwB01 B:541-741                                                                                                                                                                                 Pfam domains (1)
           Pfam domains (2) Flu_PB2-3khwB02 B:541-741                                                                                                                                                                                 Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh...........eeeee....eeeee.......eeee....eeee..eeeee...................eeeeee.hhhhh...hhhhh.......eeeeeee..eeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3khw B 541 GPESVLVNTYQWIIRNWEIVKIQWSQDPTMLYNKMEFEPFQSLVPKATRSRYSGFVRTLFQQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGLRILVRGNSPVFNYNKATKRLTVLGKDAGALTEDPDEGTSGVESAVLRGFLILGKEDKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRDS 741
                                   550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740 

   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 3KHW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (C3W6M3_I09A3 | C3W6M3)
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 Specified in the PDB File

3kc6 SAME PROTEIN DOMAIN FROM H5N1 STRAIN A/VIET NAM/1203/2004 RELATED ID: INVAE.07055.A RELATED DB: TARGETDB