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(-) Description

Title :  TOMATO SPOTTED WILT TOSPOVIRUS NUCLEOCAPSID PROTEIN-SSRNA COMPLEX
 
Authors :  K. Komoda, M. Narita, K. Yamashita, I. Tanaka, M. Yao
Date :  09 Mar 16  (Deposition) - 22 Mar 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Viral Protein, Nucleocapsid Protein, Bunyavirus, Tospovirus, Viral Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Komoda, M. Narita, K. Yamashita, I. Tanaka, M. Yao
Crystal Structure Of Tswv Nucleocapsid Protein
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NUCLEOPROTEIN
    Chains: B, C, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: B834 (DE3) PRARE2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: TSWV
    Organism Scientific: TOMATO SPOTTED WILT VIRUS
    Organism Taxid: 11613
    Synonym: NUCLEOCAPSID PROTEIN
 
Molecule 2 - RNA (5'- R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
    Chains: E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - RNA (5'-D(P*UP*UP*U)-3')
    Chains: F, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5IP2)

(-) Sites  (0, 0)

(no "Site" information available for 5IP2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IP2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5IP2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IP2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IP2)

(-) Exons   (0, 0)

(no "Exon" information available for 5IP2)

(-) 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:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.eee..eee............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ip2 A   2 SKVKLTKENIVALLTQGKDLEFNFKTFCLENLDQIKKMSIISCLTFLKNRQSIMKVIKQSDFTFGKITIKKTSDRIGATDMTFRRLDSLIRVRLVEETGNSENLNTIKSKIASHPLIQAYGLPLDDAKSVRLAIMLGGSLPLIASVDSFEMISVVLAIYQDAKYKDLGIDPKKYDTKEALGKVCTVLKSKAFEMNEDQVKKGKEYAAILSSSNSVAMEHYSETLNKFYE 244
                                    11        21 ||     40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  ||   235         
                                                23|                                                                                                                                                                                           223|               
                                                 33                                                                                                                                                                                            229               


Chain B from PDB  Type:PROTEIN  Length:233
                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee..eee............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ip2 B   2 SKVKLTKENIVALLTQGKDLEFNFKTFCLENLDQIKKMSIISCLTFLKNRQSIMKVIKQSDFTFGKITIKKTSDRIGATDMTFRRLDSLIRVRLVEETGNSENLNTIKSKIASHPLIQAYGLPLDDAKSVRLAIMLGGSLPLIASVDSFEMISVVLAIYQDAKYKDLGIDPKKYDTKEALGKVCTVLKSKAFEMNEDQVKKGKEYAAILSSSNSVAMEHYSETLNKFYEMFGV 248
                                    11        21 ||     40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  ||   235       245   
                                                23|                                                                                                                                                                                           223|                   
                                                 33                                                                                                                                                                                            229                   


Chain C from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...eee..eee............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ip2 C   2 SKVKLTKENIVALLTQGKDLEFNFKTFCLENLDQIKKMSIISCLTFLKNRQSIMKVIKQSDFTFGKITIKKTSDRIGATDMTFRRLDSLIRVRLVEETGNSENLNTIKSKIASHPLIQAYGLPLDDAKSVRLAIMLGGSLPLIASVDSFEMISVVLAIYQDAKYKDLGIDPKKYDTKEALGKVCTVLKSKAFEMNEDQVKKGKEYAAILSSSNSVAMEHYSETLNKFYE 244
                                    11        21 ||     40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  ||   235         
                                                23|                                                                                                                                                                                           223|               
                                                 33                                                                                                                                                                                            229               


Chain D from PDB  Type:RNA  Length:3
                                   
                 5ip2 D   1 UUU   3


Chain E from PDB  Type:RNA  Length:5
                                     
                 5ip2 E   1 UUUUU   5


Chain F from PDB  Type:RNA  Length:3
                                   
                 5ip2 F   1 UUU   3
   Legend:   → Mismatch (orange background)
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  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 5IP2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IP2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IP2)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        F4ZD19_TSWV | F4ZD19: 5ip1 5ip3

(-) Related Entries Specified in the PDB File

4ybw 4yby 5ip1 5ip3