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(-) Description

Title :  EXONUCLEASE DOMAIN OF LASSA VIRUS NUCLEOPROTEIN BOUND TO MANGANESE
 
Authors :  K. M. Hastie, C. R. Kimberlin, M. A. Zandonatti, I. J. Macrae, E. O. Saphi
Date :  04 Jan 11  (Deposition) - 09 Feb 11  (Release) - 07 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Deddh Exonuclease, 3' Exonuclease, Arenavirus Nucleoprotein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Hastie, C. R. Kimberlin, M. A. Zandonatti, I. J. Macrae, E. O. Saphire
Structure Of The Lassa Virus Nucleoprotein Reveals A Dsrna-Specific 3' To 5' Exonuclease Activity Essential For Immune Suppression.
Proc. Natl. Acad. Sci. Usa V. 108 2396 2011
PubMed-ID: 21262835  |  Reference-DOI: 10.1073/PNAS.1016404108

(-) Compounds

Molecule 1 - NUCLEOPROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: LASV
    Organism Scientific: LASSA VIRUS
    Organism Taxid: 11622
    Strain: MOUSE/SIERRA LEONE/JOSIAH/1976
    Synonym: NUCLEOCAPSID PROTEIN, PROTEIN N

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1MN1Ligand/IonMANGANESE (II) ION
2PO41Ligand/IonPHOSPHATE ION
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:399 , CYS A:506 , HIS A:509 , CYS A:529BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWAREHOH A:114 , HOH A:208 , ASP A:389 , ILE A:390 , GLU A:391 , ASP A:533BINDING SITE FOR RESIDUE MN A 2
3AC3SOFTWAREHOH A:56 , HOH A:81 , HOH A:113 , TYR A:410 , HIS A:412 , LEU A:505 , ALA A:552BINDING SITE FOR RESIDUE PO4 A 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q7C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q7C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q7C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q7C)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q7C)

(-) 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:209
 aligned with NCAP_LASSJ | P13699 from UniProtKB/Swiss-Prot  Length:569

    Alignment length:210
                                   369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569
           NCAP_LASSJ   360 GFTAGLTYSQLMTLKDAMLQLDPNAKTWMDIEGRPEDPVEIALYQPSSGCYIHFFREPTDLKQFKQDAKYSHGIDVTDLFATQPGLTSAVIDALPRNMVITCQGSDDIRKLLESQGRKDIKLIDIALSKTDSRKYENAVWDQYKDLCHMHTGVVVEKKKRGGKEEITPHCALMDCIMFDAAVSGGLNTSVLRAVLPRDMVFRTSTPRVVL 569
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains Arena_nucleocap-3q7cA01 A:360-544                                                                                                                                                        ------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh........eeeee.......eeeeee....eeeeee....hhhhhhhhhhhh...hhhhhh....hhhhhhhhhh....eeee.hhhhhhhhhhhh.....eeee...hhhhhh.hhhhhhhhhhhhh......ee.........ee...hhhhhhhhhhhhhhh....-..ee..hhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3q7c A 360 GFTAGLTYSQLMTLKDAMLQLDPNAKTWMDIEGRPEDPVEIALYQPSSGCYIHFFREPTDLKQFKQDAKYSHGIDVTDLFATQPGLTSAVIDALPRNMVITCQGSDDIRKLLESQGRKDIKLIDIALSKTDSRKYENAVWDQYKDLCHMHTGVVVEKKKRGGKEEITPHCALMDCIMFDAAVSGGLNT-VLRAVLPRDMVFRTSTPRVVL 569
                                   369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569
                                                                                                                                                                                                                     547 |                    
                                                                                                                                                                                                                       549
   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 3Q7C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q7C)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Arena_nucleocap] (6)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NCAP_LASSJ | P13699)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0039696    RNA-templated viral transcription    A transcription process that uses viral RNA as a template.
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0039689    negative stranded viral RNA replication    A viral genome replication process where the template genome is negative stranded, single stranded RNA ((-)ssRNA).
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0039724    suppression by virus of host IKBKE activity    Any process in which a virus stops, prevents, or reduces the activity of the host I-kappa-B kinase epsilon (IKBKE/IKK-epsilon/IKK-E).
    GO:0039548    suppression by virus of host IRF3 activity    Any process in which a virus stops, prevents, or reduces the activity of host IRF3 (interferon regulatory factor-3), a transcription factor in the RIG-I/MDA-5 signaling pathway. Viral infection triggers phosphorylation of cytoplasmic IRF3, which allows IRF3 to form a homodimer, migrate to the nucleus, and activate transcription of IFN-alpha and IFN-beta genes.
    GO:0039503    suppression by virus of host innate immune response    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    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_LASSJ | P13699: 3mwp 3mwt 3mx2 3mx5 3q7b 4fvu 4g9z 4gv3 4gv6 4gv9

(-) Related Entries Specified in the PDB File

3q7b