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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NUCLEOCAPSID PROTEIN FROM SCHMALLENBERG VIRUS
 
Authors :  A. Ariza, S. J. Tanner, C. T. Walter, K. C. Dent, D. A. Shepherd, W. Wu, S. V. Matthews, J. A. Hiscox, T. J. Green, M. Luo, R. M. Elliot, A. E. Ashc N. J. Stonehouse, N. A. Ranson, J. N. Barr, T. A. Edwards
Date :  29 Jan 13  (Deposition) - 01 May 13  (Release) - 14 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Viral Protein, Orthobunyavirus, Nucleoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ariza, S. J. Tanner, C. T. Walter, K. C. Dent, D. A. Shepherd, W. Wu, S. V. Matthews, J. A. Hiscox, T. J. Green, M. Luo, R. M. Elliott, A. R. Fooks, A. E. Ashcroft, N. J. Stonehouse, N. A. Ranson, J. N. Barr, T. A. Edwards
Nucleocapsid Protein Structures From Orthobunyaviruses Reveal Insight Into Ribonucleoprotein Architecture And Rna Polymerization.
Nucleic Acids Res. V. 41 5912 2013
PubMed-ID: 23595147  |  Reference-DOI: 10.1093/NAR/GKT268

(-) Compounds

Molecule 1 - NUCLEOCAPSID PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: CODONPLUS-RIL
    Expression System Vector: PET28-SUMO
    Expression System Vector Type: PLASMID
    Organism Scientific: SCHMALLENBERG VIRUS
    Organism Taxid: 1133363
    Other Details: CODON-OPTIMISED CDNA ENCODING THE SBV NUCLEOCAPSID PROTEIN WAS CHEMICALLY SYNTHESISED (DUNDEE CELL PRODUCTS).
    Variant: BH80/11-1 ISOLATE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3ZL9)

(-) Sites  (0, 0)

(no "Site" information available for 3ZL9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZL9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZL9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZL9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZL9)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZL9)

(-) 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:226
 aligned with NCAP_SBVBH | H2AM13 from UniProtKB/Swiss-Prot  Length:233

    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_SBVBH     3 SQFIFEDVPQRNAATFNPEVGYVAFIGKYGQQLNFGVARVFFLNQKKAKMVLHKTAQPSVDLTFGGVKFTVVNNHFPQYVSNPVPDNAITLHRMSGYLARWIADTCKASVLKLAEASAQIVMPLAEVKGCTWADGYTMYLGFAPGAEMFLDAFDFYPLVIEMHRVLKDNMDVNFMKKVLRQRYGTMTAEEWMTQKITEIKAAFNSVGQLAWAKSGFSPAARTFLQQFGINI 233
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....-----..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee...hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zl9 A   3 SQFIFEDVP-----TFNPEVGYVAFIGKYGQQLNFGVARVFFLNQKKAKMVLHKTAQPSVDLTFGGVKFTVVNNHFPQYVSNPVPDNAITLHRMSGYLARWIADTCKASVLKLAEASAQIVMPLAEVKGCTWADGYTMYLGFAPGAEMFLDAFDFYPLVIEMHRVLKDNMDVNFMKKVLRQRYGTMTAEEWMTQKITEIKAAFNSVGQLAWAKSGFSPAARTFLQQFGINI 233
                                    |-    |   22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 
                                   11    17                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:226
 aligned with NCAP_SBVBH | H2AM13 from UniProtKB/Swiss-Prot  Length:233

    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_SBVBH     2 SSQFIFEDVPQRNAATFNPEVGYVAFIGKYGQQLNFGVARVFFLNQKKAKMVLHKTAQPSVDLTFGGVKFTVVNNHFPQYVSNPVPDNAITLHRMSGYLARWIADTCKASVLKLAEASAQIVMPLAEVKGCTWADGYTMYLGFAPGAEMFLDAFDFYPLVIEMHRVLKDNMDVNFMKKVLRQRYGTMTAEEWMTQKITEIKAAFNSVGQLAWAKSGFSPAARTFLQQFGINI 233
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee...hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zl9 B   2 SSQFIFEDV------TFNPEVGYVAFIGKYGQQLNFGVARVFFLNQKKAKMVLHKTAQPSVDLTFGGVKFTVVNNHFPQYVSNPVPDNAITLHRMSGYLARWIADTCKASVLKLAEASAQIVMPLAEVKGCTWADGYTMYLGFAPGAEMFLDAFDFYPLVIEMHRVLKDNMDVNFMKKVLRQRYGTMTAEEWMTQKITEIKAAFNSVGQLAWAKSGFSPAARTFLQQFGINI 233
                                    |-     |  21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  
                                   10     17                                                                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:227
 aligned with NCAP_SBVBH | H2AM13 from UniProtKB/Swiss-Prot  Length:233

    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_SBVBH     3 SQFIFEDVPQRNAATFNPEVGYVAFIGKYGQQLNFGVARVFFLNQKKAKMVLHKTAQPSVDLTFGGVKFTVVNNHFPQYVSNPVPDNAITLHRMSGYLARWIADTCKASVLKLAEASAQIVMPLAEVKGCTWADGYTMYLGFAPGAEMFLDAFDFYPLVIEMHRVLKDNMDVNFMKKVLRQRYGTMTAEEWMTQKITEIKAAFNSVGQLAWAKSGFSPAARTFLQQFGINI 233
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....----...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee...hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zl9 C   3 SQFIFEDVP----ATFNPEVGYVAFIGKYGQQLNFGVARVFFLNQKKAKMVLHKTAQPSVDLTFGGVKFTVVNNHFPQYVSNPVPDNAITLHRMSGYLARWIADTCKASVLKLAEASAQIVMPLAEVKGCTWADGYTMYLGFAPGAEMFLDAFDFYPLVIEMHRVLKDNMDVNFMKKVLRQRYGTMTAEEWMTQKITEIKAAFNSVGQLAWAKSGFSPAARTFLQQFGINI 233
                                    |-   |    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 
                                   11   16                                                                                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:224
 aligned with NCAP_SBVBH | H2AM13 from UniProtKB/Swiss-Prot  Length:233

    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_SBVBH     3 SQFIFEDVPQRNAATFNPEVGYVAFIGKYGQQLNFGVARVFFLNQKKAKMVLHKTAQPSVDLTFGGVKFTVVNNHFPQYVSNPVPDNAITLHRMSGYLARWIADTCKASVLKLAEASAQIVMPLAEVKGCTWADGYTMYLGFAPGAEMFLDAFDFYPLVIEMHRVLKDNMDVNFMKKVLRQRYGTMTAEEWMTQKITEIKAAFNSVGQLAWAKSGFSPAARTFLQQFGINI 233
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..-------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee...hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zl9 D   3 SQFIFED-------TFNPEVGYVAFIGKYGQQLNFGVARVFFLNQKKAKMVLHKTAQPSVDLTFGGVKFTVVNNHFPQYVSNPVPDNAITLHRMSGYLARWIADTCKASVLKLAEASAQIVMPLAEVKGCTWADGYTMYLGFAPGAEMFLDAFDFYPLVIEMHRVLKDNMDVNFMKKVLRQRYGTMTAEEWMTQKITEIKAAFNSVGQLAWAKSGFSPAARTFLQQFGINI 233
                                  |  -    |   22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 
                                  9      17
   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 3ZL9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZL9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZL9)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (NCAP_SBVBH | H2AM13)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
cellular component
    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_SBVBH | H2AM13: 4idu 4idx 4jng

(-) Related Entries Specified in the PDB File

3zla CRYSTAL STRUCTURE OF THE NUCLEOCAPSID PROTEIN FROM BUNYAMWERA VIRUS BOUND TO RNA