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(-) Description

Title :  1.8A CRYSTAL STRUCTURE OF LASSA VIRUS NUCLEOPROTEIN IN COMPLEX WITH SSRNA
 
Authors :  K. M. Hastie, T. Liu, L. B. King, N. Ngo, M. A. Zandonatti, V. L. Woods, J. C Torre, E. O. Saphire
Date :  27 Jul 11  (Deposition) - 11 Jan 12  (Release) - 11 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Ssrna, Single Stranded Rna, Viral Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Hastie, T. Liu, S. Li, L. B. King, N. Ngo, M. A. Zandonatti, V. L. Woods, J. C. De La Torre, E. O. Saphire
Crystal Structure Of The Lassa Virus Nucleoprotein-Rna Complex Reveals A Gating Mechanism For Rna Binding.
Proc. Natl. Acad. Sci. Usa V. 108 19365 2011
PubMed-ID: 22084115  |  Reference-DOI: 10.1073/PNAS.1108515108

(-) Compounds

Molecule 1 - NUCLEOPROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PET46
    Fragment: N-TERMINAL DOMAIN
    Gene: NP
    Organism Scientific: MOPEIA LASSA REASSORTANT 29
    Organism Taxid: 300180
    Synonym: NUCLEOCAPSID PROTEIN
 
Molecule 2 - RNA (5'-R(P*UP*AP*UP*CP*UP*C)-3')
    Chains: C
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: H20

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NI2Ligand/IonNICKEL (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:204 , HIS A:226 , HOH A:429 , HOH A:485 , HOH A:488BINDING SITE FOR RESIDUE NI A 341
2AC2SOFTWAREHIS A:40 , GLU A:57 , HOH A:465BINDING SITE FOR RESIDUE NI A 342

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T5N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3T5N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T5N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3T5N)

(-) Exons   (0, 0)

(no "Exon" information available for 3T5N)

(-) 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:282
 aligned with Q5S585_9VIRU | Q5S585 from UniProtKB/TrEMBL  Length:569

    Alignment length:332
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337  
         Q5S585_9VIRU     8 KSFLWTQSLRRELSGYCSNIKLQVVKDAQALLHGLDFSEVSNVQRLMRKERRDDNDLKRLRDLNQAVNNLVELKSTQQKSILRVGTLTSDDLLILAADLEKLKSKVIRTERPLSAGVYMGNLSSQQLDQRRALLNMIGMSGGNQGARAGRDGVVRVWDVKNAELLSNQFGTMPSLTLACLTKQGQVDLNDAVQALTDLGLIYTAKYPNTSDLDRLTQSHPILNMIDTKKSSLNISGYNFSLGAAVKAGACMLDGGNMLETIKVSPQTMDGILKSILKVKKALGMFISDTPGERNPYENILYKICLSGDGWPYIASRTSITGRAWENTVVDLE 339
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhh........eee.....hhhhhhhhhhhhhhhhhh--------------------------------------------------.ee..hhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhh......hhhhh.....hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh................hhhhheee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t5n A   8 KSFLWTQSLRRELSGYCSNIKLQVVKDAQALLHGLDFSEVSNVQRLMRKERRDDNDLKRLRDLNQAVNNLVELKSTQQKSILRVGTLTSDDLLILAADLEKLKSK--------------------------------------------------VWDVKNAELLSNQFGTMPSLTLACLTKQGQVDLNDAVQALTDLGLIYTAKYPNTSDLDRLTQSHPILNMIDTKKSSLNISGYNFSLGAAVKAGACMLDGGNMLETIKVSPQTMDGILKSILKVKKALGMFISDTPGERNPYENILYKICLSGDGWPYIASRTSITGRAWENTVVDLE 339
                                    17        27        37        47        57        67        77        87        97       107    |    -         -         -         -         -     | 167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337  
                                                                                                                                  112                                                163                                                                                                                                                                                


Chain C from PDB  Type:RNA  Length:6
                                      
                 3t5n C   2 UAUCUC   7
   Legend:   → Mismatch (orange background)
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  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 3T5N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T5N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T5N)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5S585_9VIRU | Q5S585)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    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/TrEMBL
        Q5S585_9VIRU | Q5S585: 3t5q

(-) Related Entries Specified in the PDB File

3t5q