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(-) Description

Title :  CRYSTAL STRUCTURE OF RESTON EBOLAVIRUS VP35 RNA BINDING DOMAIN IN COMPLEX WITH 18BP DSRNA
 
Authors :  C. R. Kimberlin, Z. A. Bornholdt, S. Li, V. L. Woods, I. J. Macrae, E. O. Saphire
Date :  20 Nov 09  (Deposition) - 12 Jan 10  (Release) - 12 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E,F  (1x)
Biol. Unit 2:  C,D,E,F  (1x)
Keywords :  Ebolavirus, Rna-Binding Protein, Protein-Rna Complex, Interferon, Reston, Host Cytoplasm, Interferon Antiviral System Evasion, Rna Replication, Rna-Binding, Transcription, Virion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. R. Kimberlin, Z. A. Bornholdt, S. Li, V. L. Woods, I. J. Macrae, E. O. Saphire
Ebolavirus Vp35 Uses A Bimodal Strategy To Bind Dsrna For Innate Immune Suppression.
Proc. Natl. Acad. Sci. Usa V. 107 314 2009
PubMed-ID: 20018665  |  Reference-DOI: 10.1073/PNAS.0910547107
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- R(*AP*GP*AP*AP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*A)- 3'
    Chains: E
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'- R(*UP*CP*CP*UP*CP*CP*CP*UP*CP*CP*CP*UP*CP*CP*UP*UP*CP*U)- 3'
    Chains: F
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - POLYMERASE COFACTOR VP35
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET46 EK/LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL RNA BINDING DOMAIN (UNP RESIDUES 160- 329)
    Gene: REBOVGP2, VP35
    Organism Common: REBOV
    Organism Scientific: RESTON EBOLAVIRUS
    Organism Taxid: 129003
    Strain: RESTON

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB  EF
Biological Unit 2 (1x):   CDEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3KS8)

(-) Sites  (0, 0)

(no "Site" information available for 3KS8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KS8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KS8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KS8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KS8)

(-) Exons   (0, 0)

(no "Exon" information available for 3KS8)

(-) 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:122
 aligned with VP35_EBORR | Q8JPY0 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:122
                                   217       227       237       247       257       267       277       287       297       307       317       327  
           VP35_EBORR   208 ISAKDLKEIMYDHLPGFGTAFHQLVQVICKIGKDNNLLDTIHAEFQASLADGDSPQCALIQITKRVPIFQDVPPPIIHIRSRGDIPRACQKSLRPAPPSPKIDRGWVCLFKMQDGKTLGLKI 329
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....eee..hhhhhhhhhhh.ee......hhhh.eeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ks8 A 208 ISAKDLKEIMYDHLPGFGTAFHQLVQVICKIGKDNNLLDTIHAEFQASLADGDSPQCALIQITKRVPIFQDVPPPIIHIRSRGDIPRACQKSLRPAPPSPKIDRGWVCLFKMQDGKTLGLKI 329
                                   217       227       237       247       257       267       277       287       297       307       317       327  


Chain B from PDB  Type:PROTEIN  Length:124
 aligned with VP35_EBORR | Q8JPY0 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:124
                                   215       225       235       245       255       265       275       285       295       305       315       325    
           VP35_EBORR   206 PYISAKDLKEIMYDHLPGFGTAFHQLVQVICKIGKDNNLLDTIHAEFQASLADGDSPQCALIQITKRVPIFQDVPPPIIHIRSRGDIPRACQKSLRPAPPSPKIDRGWVCLFKMQDGKTLGLKI 329
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....eee..hhhhhhhhhhh.ee......hhhh.eeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ks8 B 206 PYISAKDLKEIMYDHLPGFGTAFHQLVQVICKIGKDNNLLDTIHAEFQASLADGDSPQCALIQITKRVPIFQDVPPPIIHIRSRGDIPRACQKSLRPAPPSPKIDRGWVCLFKMQDGKTLGLKI 329
                                   215       225       235       245       255       265       275       285       295       305       315       325    


Chain C from PDB  Type:PROTEIN  Length:122
 aligned with VP35_EBORR | Q8JPY0 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:122
                                   217       227       237       247       257       267       277       287       297       307       317       327  
           VP35_EBORR   208 ISAKDLKEIMYDHLPGFGTAFHQLVQVICKIGKDNNLLDTIHAEFQASLADGDSPQCALIQITKRVPIFQDVPPPIIHIRSRGDIPRACQKSLRPAPPSPKIDRGWVCLFKMQDGKTLGLKI 329
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....eee..hhhhhhhhhhh.ee......hhhh.eeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ks8 C 208 ISAKDLKEIMYDHLPGFGTAFHQLVQVICKIGKDNNLLDTIHAEFQASLADGDSPQCALIQITKRVPIFQDVPPPIIHIRSRGDIPRACQKSLRPAPPSPKIDRGWVCLFKMQDGKTLGLKI 329
                                   217       227       237       247       257       267       277       287       297       307       317       327  


Chain D from PDB  Type:PROTEIN  Length:124
 aligned with VP35_EBORR | Q8JPY0 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:124
                                   215       225       235       245       255       265       275       285       295       305       315       325    
           VP35_EBORR   206 PYISAKDLKEIMYDHLPGFGTAFHQLVQVICKIGKDNNLLDTIHAEFQASLADGDSPQCALIQITKRVPIFQDVPPPIIHIRSRGDIPRACQKSLRPAPPSPKIDRGWVCLFKMQDGKTLGLKI 329
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Filo_VP35-3ks8D01 D:206-329                                                                                                  Pfam domains (1)
           Pfam domains (2) Filo_VP35-3ks8D02 D:206-329                                                                                                  Pfam domains (2)
           Pfam domains (3) Filo_VP35-3ks8D03 D:206-329                                                                                                  Pfam domains (3)
           Pfam domains (4) Filo_VP35-3ks8D04 D:206-329                                                                                                  Pfam domains (4)
         Sec.struct. author ...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....eee..hhhhhhhhhhh.ee......hhhh.eeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ks8 D 206 PYISAKDLKEIMYDHLPGFGTAFHQLVQVICKIGKDNNLLDTIHAEFQASLADGDSPQCALIQITKRVPIFQDVPPPIIHIRSRGDIPRACQKSLRPAPPSPKIDRGWVCLFKMQDGKTLGLKI 329
                                   215       225       235       245       255       265       275       285       295       305       315       325    


Chain E from PDB  Type:RNA  Length:18
                                                  
                 3ks8 E   1 AGAAGGAGGGAGGGAGGA  18
                                    10        


Chain F from PDB  Type:RNA  Length:18
                                                  
                 3ks8 F   1 UCCUCCCUCCCUCCUUCU  18
                                    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 3KS8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KS8)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: Filo_VP35] (7)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (VP35_EBORR | Q8JPY0)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
    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: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:0039557    suppression by virus of host IRF7 activity    Any process in which a virus stops, prevents, or reduces the activity of host IRF7 (interferon regulatory factor-7), a transcription factor in the RIG-I/MDA-5 signaling pathway. Viral infection triggers phosphorylation of cytoplasmic IRF7, which allows IRF7 to form a homodimer, migrate to the nucleus, and activate transcription of IFN-alpha and IFN-beta genes.
    GO:0039723    suppression by virus of host TBK1 activity    Any process in which a virus stops, prevents, or reduces the activity of the host serine/threonine kinase TBK1.
    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:0039722    suppression by virus of host toll-like receptor signaling pathway    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of toll-like receptor (TLR) signaling in the host organism.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    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:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    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
        VP35_EBORR | Q8JPY0: 3ks4 3l2a 4lg2

(-) Related Entries Specified in the PDB File

3fke STRUCTURE OF ZAIRE EBOLAVIRUS VP35 IID
3ks4 CRYSTAL STRUCTURE OF RESTON EBOLAVIRUS VP35 RNA BINDING DOMAIN