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(-) Description

Title :  STRUCTURE OF THE NUCLEOPROTEIN FROM RIFT VALLEY FEVER VIRUS
 
Authors :  F. Ferron, E. I. Danek, Z. Li, D. Luo, Y. H. Wong, B. Coutard, V. Lantez, R. B. Canard, T. Walz, J. Lescar
Date :  16 Sep 10  (Deposition) - 25 May 11  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (3x)
Biol. Unit 2:  C  (6x)
Keywords :  Orthogonal Bundle, Viral Genomic Encapsidation, Viral Rna Viral Nucleoprotein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Ferron, Z. Li, E. I. Danek, D. Luo, Y. Wong, B. Coutard, V. Lantez, R. Charrel, B. Canard, T. Walz, J. Lescar
The Hexamer Structure Of Rift Valley Fever Virus Nucleoprotein Suggests A Mechanism For Its Assembly Into Ribonucleoprotein Complexes
Plos Pathog. V. 7 02030 2011
PubMed-ID: 21589902  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1002030

(-) Compounds

Molecule 1 - NUCLEOPROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: N
    Organism Common: RVFV
    Organism Scientific: RIFT VALLEY FEVER VIRUS
    Organism Taxid: 11589
    Strain: ZH-548 M12
    Synonym: NUCLEOCAPSID PROTEIN, PROTEIN N

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (3x): AB 
Biological Unit 2 (6x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
2NO23Ligand/IonNITRITE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2NO26Ligand/IonNITRITE ION
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2NO26Ligand/IonNITRITE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:32 , PHE A:33 , ALA A:202 , ALA A:203 , SER A:206 , HOH A:258 , HOH A:259 , HOH A:328 , HOH A:336BINDING SITE FOR RESIDUE NO2 A 246
2AC2SOFTWARESER A:206 , ILE A:209 , HOH A:564BINDING SITE FOR RESIDUE NA A 247
3AC3SOFTWAREGLN B:31 , GLY B:32 , PHE B:33 , ALA B:202 , ALA B:203 , SER B:206 , HOH B:258 , HOH B:262 , HOH B:278 , HOH B:358BINDING SITE FOR RESIDUE NO2 B 246
4AC4SOFTWAREHOH A:960 , ALA B:109 , SER B:148 , GLY B:151 , HOH B:356BINDING SITE FOR RESIDUE NA B 247
5AC5SOFTWAREGLY C:32 , PHE C:33 , ALA C:202 , ALA C:203 , SER C:206 , HOH C:262 , HOH C:284 , HOH C:400BINDING SITE FOR RESIDUE NO2 C 246

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OV9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OV9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OV9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OV9)

(-) Exons   (0, 0)

(no "Exon" information available for 3OV9)

(-) 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:245
 aligned with NCAP_RVFVZ | P21700 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
           NCAP_RVFVZ     1 MDNYQELRVQFAAQAVDRNEIEQWVREFAYQGFDARRVIELLKQYGGADWEKDAKKMIVLALTRGNKPRRMMMKMSKEGKATVEALINKYKLKEGNPSRDELTLSRVAAALAGWTCQALVVLSEWLPVTGTTMDGLSPAYPRHMMHPSFAGMVDPSLPGDYLRAILDAHSLYLLQFSRVINPNLRGRTKEEVAATFTQPMNAAVNSNFISHEKRREFLKAFGLVDSNGKPSAAVMAAAQAYKTAA 245
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ov9 A   1 MDNYQELRVQFAAQAVDRNEIEQWVREFAYQGFDARRVIELLKQYGGADWEKDAKKMIVLALTRGNKPRRMMMKMSKEGKATVEALINKYKLKEGNPSRDELTLSRVAAALAGWTCQALVVLSEWLPVTGTTMDGLSPAYPRHMMHPSFAGMVDPSLPGDYLRAILDAHSLYLLQFSRVINPNLRGRTKEEVAATFTQPMNAAVNSNFISHEKRREFLKAFGLVDSNGKPSAAVMAAAQAYKTAA 245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     


Chain B from PDB  Type:PROTEIN  Length:244
 aligned with NCAP_RVFVZ | P21700 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    
           NCAP_RVFVZ     2 DNYQELRVQFAAQAVDRNEIEQWVREFAYQGFDARRVIELLKQYGGADWEKDAKKMIVLALTRGNKPRRMMMKMSKEGKATVEALINKYKLKEGNPSRDELTLSRVAAALAGWTCQALVVLSEWLPVTGTTMDGLSPAYPRHMMHPSFAGMVDPSLPGDYLRAILDAHSLYLLQFSRVINPNLRGRTKEEVAATFTQPMNAAVNSNFISHEKRREFLKAFGLVDSNGKPSAAVMAAAQAYKTAA 245
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ov9 B   2 DNYQELRVQFAAQAVDRNEIEQWVREFAYQGFDARRVIELLKQYGGADWEKDAKKMIVLALTRGNKPRRMMMKMSKEGKATVEALINKYKLKEGNPSRDELTLSRVAAALAGWTCQALVVLSEWLPVTGTTMDGLSPAYPRHMMHPSFAGMVDPSLPGDYLRAILDAHSLYLLQFSRVINPNLRGRTKEEVAATFTQPMNAAVNSNFISHEKRREFLKAFGLVDSNGKPSAAVMAAAQAYKTAA 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
 aligned with NCAP_RVFVZ | P21700 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    
           NCAP_RVFVZ     2 DNYQELRVQFAAQAVDRNEIEQWVREFAYQGFDARRVIELLKQYGGADWEKDAKKMIVLALTRGNKPRRMMMKMSKEGKATVEALINKYKLKEGNPSRDELTLSRVAAALAGWTCQALVVLSEWLPVTGTTMDGLSPAYPRHMMHPSFAGMVDPSLPGDYLRAILDAHSLYLLQFSRVINPNLRGRTKEEVAATFTQPMNAAVNSNFISHEKRREFLKAFGLVDSNGKPSAAVMAAAQAYKTAA 245
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Tenui_N-3ov9C01 C:3-223                                                                                                                                                                                                      ---------------------- Pfam domains (1)
           Pfam domains (2) -Tenui_N-3ov9C02 C:3-223                                                                                                                                                                                                      ---------------------- Pfam domains (2)
           Pfam domains (3) -Tenui_N-3ov9C03 C:3-223                                                                                                                                                                                                      ---------------------- Pfam domains (3)
         Sec.struct. author .hhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ov9 C   2 DNYQELRVQFAAQAVDRNEIEQWVREFAYQGFDARRVIELLKQYGGADWEKDAKKMIVLALTRGNKPRRMMMKMSKEGKATVEALINKYKLKEGNPSRDELTLSRVAAALAGWTCQALVVLSEWLPVTGTTMDGLSPAYPRHMMHPSFAGMVDPSLPGDYLRAILDAHSLYLLQFSRVINPNLRGRTKEEVAATFTQPMNAAVNSNFISHEKRREFLKAFGLVDSNGKPSAAVMAAAQAYKTAA 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
   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 3OV9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OV9)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: Tenui_N] (3)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (NCAP_RVFVZ | P21700)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
cellular component
    GO:0019029    helical viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles; the subunits are arranged to form a protein helix with the genetic material contained within. Tobacco mosaic virus has such a capsid structure.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    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_RVFVZ | P21700: 3ouo

(-) Related Entries Specified in the PDB File

3ouo N RIFT VALLEY FEVER VIRUS