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(-) Description

Title :  TOMATO SPOTTED WILT TOSPOVIRUS NUCLEOCAPSID PROTEIN-SSDNA 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 :  3.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Viral Protein, Nucleocapsid Protein, Bunyavirus, Tospovirus, Viral Protein-Dna 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 - DNA (5'-D(P*TP*TP*TP*TP*T)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')
    Chains: E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
    Chains: F
    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 5IP3)

(-) Sites  (0, 0)

(no "Site" information available for 5IP3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IP3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5IP3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IP3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IP3)

(-) Exons   (0, 0)

(no "Exon" information available for 5IP3)

(-) 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:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh............hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...eee..eee........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...........hhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ip3 A   3 KVKLTKENIVALLTQGKDLEFEENVAFNFKTFCLENLDQIKKMSIISCLTFLKNRQSIMKVIKQSDFTFGKITIDRIGATDMTFRRLDSLIRVRLVEETGNSENLNTIKSKIASHPLIQAYGLPLDDAKSVRLAIMLGGSLPLIASVDSFEMISVVLAIYQDAKYKDLGIDPKKYDTKEALGKVCTVLKSKAFEMNEDQVKKGKEYAAILSSSNPNAKGSVAMEHYSETLNKFYEMFGVKK 250
                                    12        22   ||   35        45        55        65        75   ||   89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249 
                                                  26|                                               79|                                                                                                                                                                      
                                                   30                                                84                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhh............hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....ee..ee.............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...........hhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.............hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ip3 B   4 VKLTKENIVALLTQGKDLEFENLVAFNFKTFCLENLDQIKKMSIISCLTFLKNRQSIMKVIKQSDFTFGKITIKKTSDRIGATDMTFRRLDSLIRVRLVEETGNSENLNTIKSKIASHPLIQAYGLPLDDAKSVRLAIMLGGSLPLIASVDSFEMISVVLAIYQDAKYKDLGIDPKKYDTKEALGKVCTVLKSKAFEMNEDQVKKGKEYAAILSSSNPNAKGSVAMEHYSETLNKFYEMFGVKKQA 252
                                    13        23||      36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246      
                                               24|                                                                                                                                                                                                                                
                                                28                                                                                                                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhh.........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..eee..eee.........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhh.....hhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ip3 C   2 SKVKLTKENIVALLTQGKDLEFEENFKTFCLENLDQIKKMSIISCLTFLKNRQSIMKVIKQSDFTFGKITIKKRIGATDMTFRRLDSLIRVRLVEETGNSENLNTIKSKIASHPLIQAYGLPLDDAKSVRLAIMLGGSLPLIASVDSFEMISVVLAIYQDAKYKDLGIDPKKYDTKEALGKVCTVLKSKAFEMNEDQVKKGKEYAAILSSSNPNAKGSVAMEHYSETLNKFYEMFGVKKQAKLAEL 257
                                    11        21   ||   38        48        58        68        78  ||    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
                                                  25|                                              81|                                                                                                                                                                            
                                                   33                                               85                                                                                                                                                                            


Chain D from PDB  Type:DNA  Length:5
                                     
                 5ip3 D   1 TTTTT   5


Chain E from PDB  Type:DNA  Length:7
                                       
                 5ip3 E   1 TTTTTTT   7


Chain F from PDB  Type:DNA  Length:6
                                      
                 5ip3 F   1 TTTTTT   6
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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 5IP3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IP3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IP3)

(-) 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 5ip2

(-) Related Entries Specified in the PDB File

4ybw 4ybx 5ip1 5ip2