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(-) Description

Title :  CRYSTAL STRUCTURE OF RIFT VALLEY FEVER VIRUS NUCLEOCAPSID PROTEIN TETRAMER BOUND TO SINGLE-STRANDED RNA
 
Authors :  D. D. Raymond, J. L. Smith
Date :  18 Sep 12  (Deposition) - 07 Nov 12  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (2x)
Biol. Unit 2:  C,D,F  (2x)
Keywords :  Nucleocapsid Protein, N Protein, Ribonucleoprotein, Viral Nucleoprotein, Rna Binding, Virus, Rnp, Viral Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. D. Raymond, M. E. Piper, S. R. Gerrard, G. Skiniotis, J. L. Smith
Phleboviruses Encapsidate Their Genomes By Sequestering Rna Bases.
Proc. Natl. Acad. Sci. Usa V. 109 19208 2012
PubMed-ID: 23129612  |  Reference-DOI: 10.1073/PNAS.1213553109

(-) Compounds

Molecule 1 - NUCLEOCAPSID PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSUMO
    Expression System Strain: BL21 AI/PRARE2
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: N
    Organism Common: RVFV
    Organism Scientific: RIFT VALLEY FEVER VIRUS
    Organism Taxid: 11588
    Strain: ZH-501
 
Molecule 2 - 28-MER POLY(U) RNA
    Chains: E, F
    Engineered: YES
    Fragment: SEE REMARK 999
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (2x): AB  E 
Biological Unit 2 (2x):   CD F

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4H5P)

(-) Sites  (0, 0)

(no "Site" information available for 4H5P)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H5P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4H5P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H5P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H5P)

(-) Exons   (0, 0)

(no "Exon" information available for 4H5P)

(-) 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:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhh....hhhhhhhhhhhh.........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h5p A   2 DNYQELAIQFAAQAVDRNEIEQWVREFAYQGFDARRVIELLKQYGGADWEKDAKKMIVLALTRGNKPRRMMMKMSKEGKATVEALINKYKLKEGNPSRDELTLSRVAAALAGRTCQALVVLSEWLPVTGTTMDGLSPAYPRHMMHPSFAGMVDPSLPGDYLRAILDAHSLYLLQFSRVINPNLRGRTKEEVAATFTQPMNAAVNSNFISHEKRREFLKAFGLVDSNGKPSAAVMAAAQAYKTAA 245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    


Chain B from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h5p B   2 DNYQELAIQFAAQAVDRNEIEQWVREFAYQGFDARRVIELLKQYGGADWEKDAKKMIVLALTRGNKPRRMMMKMSKEGKATVEALINKYKLKEGNPSRDELTLSRVAAALAGRTCQALVVLSEWLPVTGTTMDGLSPAYPRHMMHPSFAGMVDPSLPGDYLRAILDAHSLYLLQFSRVINPNLRGRTKEEVAATFTQPMNAAVNSNFISHEKRREFLKAFGLVDSNGKPSAAVMAAAQAYKTAA 245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    


Chain C from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h5p C   2 DNYQELAIQFAAQAVDRNEIEQWVREFAYQGFDARRVIELLKQYGGADWEKDAKKMIVLALTRGNKPRRMMMKMSKEGKATVEALINKYKLKEGNPSRDELTLSRVAAALAGRTCQALVVLSEWLPVTGTTMDGLSPAYPRHMMHPSFAGMVDPSLPGDYLRAILDAHSLYLLQFSRVINPNLRGRTKEEVAATFTQPMNAAVNSNFISHEKRREFLKAFGLVDSNGKPSAAVMAAAQAYKTAA 245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    


Chain D from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h5p D   2 DNYQELAIQFAAQAVDRNEIEQWVREFAYQGFDARRVIELLKQYGGADWEKDAKKMIVLALTRGNKPRRMMMKMSKEGKATVEALINKYKLKEGNPSRDELTLSRVAAALAGRTCQALVVLSEWLPVTGTTMDGLSPAYPRHMMHPSFAGMVDPSLPGDYLRAILDAHSLYLLQFSRVINPNLRGRTKEEVAATFTQPMNAAVNSNFISHEKRREFLKAFGLVDSNGKPSAAVMAAAQAYKTAA 245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    


Chain E from PDB  Type:RNA  Length:14
                                              
                 4h5p E   1 UUUUUUUUUUUUUU  14
                                    10    


Chain F from PDB  Type:RNA  Length:14
                                              
                 4h5p F   1 UUUUUUUUUUUUUU  14
                                    10
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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 4H5P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H5P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H5P)

(-) Gene Ontology  (2, 2)

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 Related Entries

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        D3K5I7_RVFV | D3K5I7: 3lyf 4h5m 4h5o 4h5q 4v9e

(-) Related Entries Specified in the PDB File

4h5l 4h5m 4h5o 4h5q 4h6f 4h6g