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(-) Description

Title :  CRYSTAL STRUCTURE OF RIFT VALLEY FEVER VIRUS NUCLEOCAPSID PROTEIN HEXAMER BOUND TO SINGLE-STRANDED DNA
 
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 :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Nucleocapsid Protein, N Protein, Ribonucleoprotein, Viral Nucleoprotein, Rna Binding, Virus, Rnp, Viral Protein-Dna 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
    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 - 30-MER POLY(T) DNA
    Chains: D
    Engineered: YES
    Fragment: SEE REMARK 999
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4H5Q)

(-) Sites  (0, 0)

(no "Site" information available for 4H5Q)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H5Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4H5Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H5Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H5Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4H5Q)

(-) 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:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h5q A   4 YQELAIQFAAQAVDRNEIEQWVREFAYQGFDARRVIELLKQYGGADWEKDAKKMIVLALTRGNKPRRMMMKMSKEGKATVEALINKYKLKEGNPSRDELTLSRVAAALAGRTCQALVVLSEWLPVTGTTMDGLSPAYPRHMMHPSFAGMVDPSLPGDYLRAILDAHSLYLLQFSRVINPNLRGRTKEEVAATFTQPMNAAVNSNFISHEKRREFLKAFGLVDSNGKPSAAVMAAAQAYKTAA 245
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243  


Chain B from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h5q B   3 NYQELAIQFAAQAVDRNEIEQWVREFAYQGFDARRVIELLKQYGGADWEKDAKKMIVLALTRGNKPRRMMMKMSKEGKATVEALINKYKLKEGNPSRDELTLSRVAAALAGRTCQALVVLSEWLPVTGTTMDGLSPAYPRHMMHPSFAGMVDPSLPGDYLRAILDAHSLYLLQFSRVINPNLRGRTKEEVAATFTQPMNAAVNSNFISHEKRREFLKAFGLVDSNGKPSAAVMAAAQAYKTAA 245
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242   


Chain C from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h5q C   3 NYQELAIQFAAQAVDRNEIEQWVREFAYQGFDARRVIELLKQYGGADWEKDAKKMIVLALTRGNKPRRMMMKMSKEGKATVEALINKYKLKEGNPSRDELTLSRVAAALAGRTCQALVVLSEWLPVTGTTMDGLSPAYPRHMMHPSFAGMVDPSLPGDYLRAILDAHSLYLLQFSRVINPNLRGRTKEEVAATFTQPMNAAVNSNFISHEKRREFLKAFGLVDSNGKPSAAVMAAAQAYKTAA 245
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242   


Chain D from PDB  Type:DNA  Length:14
                                              
                 4h5q D   1 TTTTTTTTTTTTTT  14
                                    10
   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 4H5Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H5Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H5Q)

(-) Gene Ontology  (2, 2)

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 Related Entries

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

UniProtKB/TrEMBL
        D3K5I7_RVFV | D3K5I7: 3lyf 4h5m 4h5o 4h5p 4v9e

(-) Related Entries Specified in the PDB File

4h5l 4h5m 4h5o 4h5p 4h6f 4h6g