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(-) Description

Title :  CRYSTAL STRUCTURE OF TETRAMER OF LA CROSSE VIRUS NUCLEOPROTEIN IN COMPLEX WITH SSRNA
 
Authors :  J. Reguera, H. Malet, F. Weber, S. Cusack
Date :  03 Apr 13  (Deposition) - 24 Apr 13  (Release) - 15 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym./Biol. Unit :  B,D,F,R,Z
Keywords :  Viral Protein-Rna Complex, Rna-Binding, Genome Packaging (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Reguera, H. Malet, F. Weber, S. Cusack
Structural Basis For Encapsidation Of Genomic Rna By La Crosse Orthobunyavirus Nucleoprotein.
Proc. Natl. Acad. Sci. Usa V. 110 7246 2013
PubMed-ID: 23589854  |  Reference-DOI: 10.1073/PNAS.1302298110

(-) Compounds

Molecule 1 - NUCLEOPROTEIN
    Chains: B, F, D, Z
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET9A
    Expression System Vector Type: PLASMID
    Organism Scientific: LA CROSSE VIRUS
    Organism Taxid: 11577
    Synonym: NUCLEOCAPSID PROTEIN, PROTEIN N
 
Molecule 2 - POLY-URIDINE 45-MER
    Chains: R
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : BDFRZ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4BHH)

(-) Sites  (0, 0)

(no "Site" information available for 4BHH)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BHH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4BHH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BHH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BHH)

(-) Exons   (0, 0)

(no "Exon" information available for 4BHH)

(-) 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 B from PDB  Type:PROTEIN  Length:231
 aligned with NCAP_BUNLC | P04873 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:231
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 
           NCAP_BUNLC     3 DLVFYDVASTGANGFDPDAGYMDFCVKNAESLNLAAVRIFFLNAAKAKAALSRKPERKANPKFGEWQVEVINNHFPGNRNNPIGNNDLTIHRLSGYLARWVLDQYNENDDESQHELIRTTIINPIAESNGVGWDSGPEIYLSFFPGTEMFLETFKFYPLTIGIHRVKQGMMDPQYLKKALRQRYGTLTADKWMSQKVAAIAKSLKDVEQLKWGKGGLSDTAKTFLQKFGIR 233
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..ee..ee..ee...hhhhh.........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhh...hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bhh B   3 DLVFYDVASTGANGFDPDAGYMDFCVKNAESLNLAAVRIFFLNAAKAKAALSRKPERKANPKFGEWQVEVINNHFPGNRNNPIGNNDLTIHRLSGYLARWVLDQYNENDDESQHELIRTTIINPIAESNGVGWDSGPEIYLSFFPGTEMFLETFKFYPLTIGIHRVKQGMMDPQYLKKALRQRYGTLTADKWMSQKVAAIAKSLKDVEQLKWGKGGLSDTAKTFLQKFGIR 233
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 


Chain D from PDB  Type:PROTEIN  Length:223
 aligned with NCAP_BUNLC | P04873 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:230
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233
           NCAP_BUNLC     4 LVFYDVASTGANGFDPDAGYMDFCVKNAESLNLAAVRIFFLNAAKAKAALSRKPERKANPKFGEWQVEVINNHFPGNRNNPIGNNDLTIHRLSGYLARWVLDQYNENDDESQHELIRTTIINPIAESNGVGWDSGPEIYLSFFPGTEMFLETFKFYPLTIGIHRVKQGMMDPQYLKKALRQRYGTLTADKWMSQKVAAIAKSLKDVEQLKWGKGGLSDTAKTFLQKFGIR 233
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..-------..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...ee..ee..ee..ee...hhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhh...hhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bhh D   4 LVFYD-------GFDPDAGYMDFCVKNAESLNLAAVRIFFLNAAKAKAALSRKPERKANPKFGEWQVEVINNHFPGNRNNPIGNNDLTIHRLSGYLARWVLDQYNENDDESQHELIRTTIINPIAESNGVGWDSGPEIYLSFFPGTEMFLETFKFYPLTIGIHRVKQGMMDPQYLKKALRQRYGTLTADKWMSQKVAAIAKSLKDVEQLKWGKGGLSDTAKTFLQKFGIR 233
                                |    -  |     23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233
                                8      16                                                                                                                                                                                                                         


Chain F from PDB  Type:PROTEIN  Length:232
 aligned with NCAP_BUNLC | P04873 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:232
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  
           NCAP_BUNLC     2 SDLVFYDVASTGANGFDPDAGYMDFCVKNAESLNLAAVRIFFLNAAKAKAALSRKPERKANPKFGEWQVEVINNHFPGNRNNPIGNNDLTIHRLSGYLARWVLDQYNENDDESQHELIRTTIINPIAESNGVGWDSGPEIYLSFFPGTEMFLETFKFYPLTIGIHRVKQGMMDPQYLKKALRQRYGTLTADKWMSQKVAAIAKSLKDVEQLKWGKGGLSDTAKTFLQKFGIR 233
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..ee..ee..ee...hhhhh.........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhh...hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bhh F   2 SDLVFYDVASTGANGFDPDAGYMDFCVKNAESLNLAAVRIFFLNAAKAKAALSRKPERKANPKFGEWQVEVINNHFPGNRNNPIGNNDLTIHRLSGYLARWVLDQYNENDDESQHELIRTTIINPIAESNGVGWDSGPEIYLSFFPGTEMFLETFKFYPLTIGIHRVKQGMMDPQYLKKALRQRYGTLTADKWMSQKVAAIAKSLKDVEQLKWGKGGLSDTAKTFLQKFGIR 233
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  


Chain R from PDB  Type:RNA  Length:44
                                                                            
                 4bhh R   1 UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU  44
                                    10        20        30        40    


Chain Z from PDB  Type:PROTEIN  Length:223
 aligned with NCAP_BUNLC | P04873 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:230
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233
           NCAP_BUNLC     4 LVFYDVASTGANGFDPDAGYMDFCVKNAESLNLAAVRIFFLNAAKAKAALSRKPERKANPKFGEWQVEVINNHFPGNRNNPIGNNDLTIHRLSGYLARWVLDQYNENDDESQHELIRTTIINPIAESNGVGWDSGPEIYLSFFPGTEMFLETFKFYPLTIGIHRVKQGMMDPQYLKKALRQRYGTLTADKWMSQKVAAIAKSLKDVEQLKWGKGGLSDTAKTFLQKFGIR 233
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..-------..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...ee..ee..ee..ee...hhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhh...hhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bhh Z   4 LVFYD-------GFDPDAGYMDFCVKNAESLNLAAVRIFFLNAAKAKAALSRKPERKANPKFGEWQVEVINNHFPGNRNNPIGNNDLTIHRLSGYLARWVLDQYNENDDESQHELIRTTIINPIAESNGVGWDSGPEIYLSFFPGTEMFLETFKFYPLTIGIHRVKQGMMDPQYLKKALRQRYGTLTADKWMSQKVAAIAKSLKDVEQLKWGKGGLSDTAKTFLQKFGIR 233
                                |    -  |     23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233
                                8      16
   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 4BHH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BHH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BHH)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B,D,F,Z   (NCAP_BUNLC | P04873)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
    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: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.
cellular component
    GO:0019029    helical viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles; the subunits are arranged to form a protein helix with the genetic material contained within. Tobacco mosaic virus has such a capsid structure.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019013    viral nucleocapsid    The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
    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
        NCAP_BUNLC | P04873: 4bgp

(-) Related Entries Specified in the PDB File

4bgp CRYSTAL STRUCTURE OF LA CROSSE VIRUS NUCLEOPROTEIN