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(-) Description

Title :  CRYSTAL STRUCTURE OF ZAIRE EBOLA VP35 INTERFERON INHIBITORY DOMAIN BOUND TO 8 BP DSRNA
 
Authors :  D. W. Leung, K. C. Prins, D. M. Borek, M. Farahbakhsh, J. M. Tufariello, P. Ramanan, J. C. Nix, L. A. Helgeson, Z. Otwinowski, R. B. Honzatko, C. F. Basler, G. K. Amarasinghe
Date :  14 Dec 09  (Deposition) - 26 Jan 10  (Release) - 16 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Rna Binding Domain, Coiled Coil, Interferon Antiviral System Evasion, Rna Replication, Rna Binding Protein, Transcription, Host Cytoplasm, Rna-Binding, Virion, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. W. Leung, K. C. Prins, D. M. Borek, M. Farahbakhsh, J. M. Tufariello, P. Ramanan, J. C. Nix, L. A. Helgeson, Z. Otwinowski, R. B. Honzatko, C. F. Basler, G. K. Amarasinghe
Structural Basis For Dsrna Recognition And Interferon Antagonism By Ebola Vp35.
Nat. Struct. Mol. Biol. V. 17 165 2010
PubMed-ID: 20081868  |  Reference-DOI: 10.1038/NSMB.1765
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - POLYMERASE COFACTOR VP35
    Chains: A, B, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: ZAIRE EBOLA VP35 INTERFERON INHIBITORY DOMAIN
    Gene: VP35
    Organism Common: ZEBOV
    Organism Scientific: ZAIRE EBOLAVIRUS
    Organism Taxid: 128952
    Strain: MAYINGA-76
 
Molecule 2 - RNA (5'-R(*CP*GP*CP*AP*UP*GP*CP*G)-3')
    Chains: C, F
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 38)

Asymmetric/Biological Unit (5, 38)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2FMT24Ligand/IonFORMIC ACID
3GOL1Ligand/IonGLYCEROL
4MG1Ligand/IonMAGNESIUM ION
5NA8Ligand/IonSODIUM ION

(-) Sites  (38, 38)

Asymmetric Unit (38, 38)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREFMT A:11 , FMT A:12 , GLY A:236 , PRO A:304BINDING SITE FOR RESIDUE MG A 1
02AC2SOFTWAREARG A:300BINDING SITE FOR RESIDUE CL A 2
03AC3SOFTWAREHOH A:32 , HOH A:185 , LEU A:232 , GLY A:234 , PHE A:235 , HOH A:353BINDING SITE FOR RESIDUE NA A 10
04AC4SOFTWAREARG A:305 , HOH A:343 , TRP E:324 , U F:5 , G F:6 , HOH F:10BINDING SITE FOR RESIDUE GOL A 341
05AC5SOFTWAREPHE A:235 , ARG A:305 , GLN B:329 , PRO E:316BINDING SITE FOR RESIDUE FMT A 3
06AC6SOFTWAREMG A:1 , TYR A:229 , HIS A:240 , GLN A:244BINDING SITE FOR RESIDUE FMT A 11
07AC7SOFTWAREMG A:1 , PHE A:235 , GLY A:236 , HIS A:240 , ASP B:332BINDING SITE FOR RESIDUE FMT A 12
08AC8SOFTWAREHOH A:28 , PRO A:293 , VAL A:294 , FMT E:8 , ARG E:305BINDING SITE FOR RESIDUE FMT A 16
09AC9SOFTWAREHOH A:33 , GLN A:274 , HOH A:363 , G C:6 , HOH C:89BINDING SITE FOR RESIDUE FMT A 19
10BC1SOFTWAREGLN B:264BINDING SITE FOR RESIDUE CL B 5
11BC2SOFTWAREHOH B:71 , LEU B:232 , PRO B:233 , GLY B:234 , PHE B:235BINDING SITE FOR RESIDUE NA B 6
12BC3SOFTWAREHOH B:29 , PRO B:315 , PRO B:316 , PRO E:315 , PRO E:316BINDING SITE FOR RESIDUE NA B 13
13BC4SOFTWAREGLY B:301 , ASP B:302BINDING SITE FOR RESIDUE FMT B 10
14BC5SOFTWAREHOH B:140 , SER B:317 , PRO B:318 , LYS B:319 , ARG B:322 , TRP B:324BINDING SITE FOR RESIDUE FMT B 341
15BC6SOFTWAREHOH B:204 , ALA B:265 , GLU B:269 , HOH B:357BINDING SITE FOR RESIDUE FMT B 17
16BC7SOFTWAREFMT B:22 , GLY B:236 , THR B:237 , GLN B:241 , GLN B:244 , PRO B:304 , CYS B:307BINDING SITE FOR RESIDUE FMT B 18
17BC8SOFTWAREFMT B:18 , PHE B:235 , GLY B:236 , HIS B:240 , HOH D:358BINDING SITE FOR RESIDUE FMT B 22
18BC9SOFTWARELYS B:282 , ASP B:321BINDING SITE FOR RESIDUE FMT B 23
19CC1SOFTWARELYS B:282 , VAL B:284 , GLN B:288BINDING SITE FOR RESIDUE FMT B 25
20CC2SOFTWAREHOH A:33 , U C:5 , HOH C:89 , HOH D:34 , U F:5 , HOH F:54BINDING SITE FOR RESIDUE NA C 9
21CC3SOFTWAREU C:5 , G C:6 , HOH C:37 , HOH C:40 , HOH C:285 , HOH F:121BINDING SITE FOR RESIDUE NA C 10
22CC4SOFTWAREC C:3 , HOH C:307 , HOH D:151 , SER D:310 , HOH D:344 , HOH D:362BINDING SITE FOR RESIDUE NA C 12
23CC5SOFTWAREC C:3 , A C:4 , HOH C:27 , HOH C:50 , HOH C:77 , HOH C:108 , THR D:237 , PHE D:239 , G F:6BINDING SITE FOR RESIDUE FMT C 11
24CC6SOFTWAREHOH A:145 , PHE A:239 , G C:6 , HOH C:36 , HOH C:107 , HOH C:124 , C F:3 , A F:4BINDING SITE FOR RESIDUE FMT C 24
25CC7SOFTWAREHIS D:231BINDING SITE FOR RESIDUE CL D 4
26CC8SOFTWAREHOH D:10 , HOH D:59 , LEU D:232 , GLY D:234 , PHE D:235 , HOH D:343BINDING SITE FOR RESIDUE NA D 8
27CC9SOFTWAREHOH D:86 , ASN D:254 , SER D:255 , LEU D:256 , ASP D:257 , ILE D:258BINDING SITE FOR RESIDUE FMT D 2
28DC1SOFTWAREU C:5 , HOH C:14 , ARG D:305 , HOH D:364 , HOH D:370BINDING SITE FOR RESIDUE FMT D 341
29DC2SOFTWAREPRO B:316 , PHE D:235 , ARG D:305 , GLN E:329 , HOH E:350BINDING SITE FOR RESIDUE FMT D 6
30DC3SOFTWAREHOH D:34 , GLN D:274 , HOH D:357 , G F:6 , HOH F:54BINDING SITE FOR RESIDUE FMT D 20
31DC4SOFTWAREARG B:305 , HOH D:199 , LEU D:249 , PRO D:293 , HOH D:360BINDING SITE FOR RESIDUE FMT D 21
32DC5SOFTWARESER E:299 , ARG E:300BINDING SITE FOR RESIDUE CL E 3
33DC6SOFTWAREGLN E:241BINDING SITE FOR RESIDUE FMT E 7
34DC7SOFTWAREFMT A:16 , HOH A:74 , VAL A:294 , HOH E:44 , ARG E:305 , ALA E:306BINDING SITE FOR RESIDUE FMT E 8
35DC8SOFTWAREPHE D:235 , GLY D:236 , HIS D:240 , ASP E:332 , GLY E:333 , HOH E:351 , HOH E:369BINDING SITE FOR RESIDUE FMT E 14
36DC9SOFTWAREHOH A:112 , ASP A:332BINDING SITE FOR RESIDUE FMT E 15
37EC1SOFTWAREHOH C:217 , U F:5 , G F:6 , HOH F:16 , HOH F:58 , HOH F:297BINDING SITE FOR RESIDUE NA F 11
38EC2SOFTWAREHOH A:178 , G F:2 , C F:3 , HOH F:142 , HOH F:175 , HOH F:316BINDING SITE FOR RESIDUE FMT F 9

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L25)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L25)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L25)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L25)

(-) Exons   (0, 0)

(no "Exon" information available for 3L25)

(-) 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:123
 aligned with VP35_EBOZM | Q05127 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:123
                                   227       237       247       257       267       277       287       297       307       317       327       337   
           VP35_EBOZM   218 DISAKDLRNIMYDHLPGFGTAFHQLVQVICKLGKDSNSLDIIHAEFQASLAEGDSPQCALIQITKRVPIFQDAAPPVIHIRSRGDIPRACQKSLRPVPPSPKIDRGWVCVFQLQDGKTLGLKI 340
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....eee..hhhhh...hhh.ee......hhhh.eeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l25 A 218 DISAKDLRNIMYDHLPGFGTAFHQLVQVICKLGKDSNSLDIIHAEFQASLAEGDSPQCALIQITKRVPIFQDAAPPVIHIRSRGDIPRACQKSLRPVPPSPKIDRGWVCVFQLQDGKTLGLKI 340
                                   227       237       247       257       267       277       287       297       307       317       327       337   


Chain B from PDB  Type:PROTEIN  Length:123
 aligned with VP35_EBOZM | Q05127 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:123
                                   227       237       247       257       267       277       287       297       307       317       327       337   
           VP35_EBOZM   218 DISAKDLRNIMYDHLPGFGTAFHQLVQVICKLGKDSNSLDIIHAEFQASLAEGDSPQCALIQITKRVPIFQDAAPPVIHIRSRGDIPRACQKSLRPVPPSPKIDRGWVCVFQLQDGKTLGLKI 340
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....eee..hhhhhhhhhhh.ee......hhhh.eeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l25 B 218 DISAKDLRNIMYDHLPGFGTAFHQLVQVICKLGKDSNSLDIIHAEFQASLAEGDSPQCALIQITKRVPIFQDAAPPVIHIRSRGDIPRACQKSLRPVPPSPKIDRGWVCVFQLQDGKTLGLKI 340
                                   227       237       247       257       267       277       287       297       307       317       327       337   


Chain C from PDB  Type:RNA  Length:8
                                        
                 3l25 C   1 CGCAUGCG   8


Chain D from PDB  Type:PROTEIN  Length:123
 aligned with VP35_EBOZM | Q05127 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:123
                                   227       237       247       257       267       277       287       297       307       317       327       337   
           VP35_EBOZM   218 DISAKDLRNIMYDHLPGFGTAFHQLVQVICKLGKDSNSLDIIHAEFQASLAEGDSPQCALIQITKRVPIFQDAAPPVIHIRSRGDIPRACQKSLRPVPPSPKIDRGWVCVFQLQDGKTLGLKI 340
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.....eeee.hhhhh...hhh.ee......hhhh.eeeeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l25 D 218 DISAKDLRNIMYDHLPGFGTAFHQLVQVICKLGKDSNSLDIIHAEFQASLAEGDSPQCALIQITKRVPIFQDAAPPVIHIRSRGDIPRACQKSLRPVPPSPKIDRGWVCVFQLQDGKTLGLKI 340
                                   227       237       247       257       267       277       287       297       307       317       327       337   


Chain E from PDB  Type:PROTEIN  Length:123
 aligned with VP35_EBOZM | Q05127 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:123
                                   227       237       247       257       267       277       287       297       307       317       327       337   
           VP35_EBOZM   218 DISAKDLRNIMYDHLPGFGTAFHQLVQVICKLGKDSNSLDIIHAEFQASLAEGDSPQCALIQITKRVPIFQDAAPPVIHIRSRGDIPRACQKSLRPVPPSPKIDRGWVCVFQLQDGKTLGLKI 340
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Filo_VP35-3l25E01 E:218-340                                                                                                 Pfam domains (1)
           Pfam domains (2) Filo_VP35-3l25E02 E:218-340                                                                                                 Pfam domains (2)
           Pfam domains (3) Filo_VP35-3l25E03 E:218-340                                                                                                 Pfam domains (3)
           Pfam domains (4) Filo_VP35-3l25E04 E:218-340                                                                                                 Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....eee..hhhhhhhhhhh.ee......hhhh.eeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l25 E 218 DISAKDLRNIMYDHLPGFGTAFHQLVQVICKLGKDSNSLDIIHAEFQASLAEGDSPQCALIQITKRVPIFQDAAPPVIHIRSRGDIPRACQKSLRPVPPSPKIDRGWVCVFQLQDGKTLGLKI 340
                                   227       237       247       257       267       277       287       297       307       317       327       337   


Chain F from PDB  Type:RNA  Length:8
                                        
                 3l25 F   1 CGCAUGCG   8
   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 3L25)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L25)

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,D,E   (VP35_EBOZM | Q05127)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0060965    negative regulation of gene silencing by miRNA    Any process that decreases the rate, frequency, or extent of the downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: mRNA cleavage or translational repression.
    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:0039549    suppression by virus of host IRF3 activity by inhibition of IRF3 phosphorylation    Any process in which a virus stops, prevents, or reduces the rate or extent of the phosphorylation of IRF3 (interferon regulatory factor-3), thereby inhibiting IRF3 activation. In response to signaling from RIG-1/MDA-5 receptors, IRF3 is phosphorylated on multiple serine and threonine residues; phosphorylation results in the cytoplasm-to-nucleus translocation of IRF3, DNA binding, and increased transcriptional activation of interferon-encoding genes.
    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:0039558    suppression by virus of host IRF7 activity by positive regulation of IRF7 sumoylation    Any process in which a virus stops, prevents, or reduces IRF7-dependent gene transcription, by promoting the sumoylation of IRF7, thereby disabling its activity.
    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:0039505    suppression by virus of host antigen processing and presentation of peptide antigen via MHC class II    Any viral process that inhibits a host antigen-presenting cell expressing a peptide antigen on its cell surface in association with an MHC class II protein complex.
    GO:0046775    suppression by virus of host cytokine production    Any viral process that results in the inhibition of host cell cytokine production.
    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:0039501    suppression by virus of host type I interferon production    Any viral process that results in the inhibition of host cell type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0044414    suppression of host defenses    Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of host defense(s) by active mechanisms that normally result in the shutting down of a host pathway. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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: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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  3l25
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  VP35_EBOZM | Q05127
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  VP35_EBOZM | Q05127
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 Related Entries

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

UniProtKB/Swiss-Prot
        VP35_EBOZM | Q05127: 3fke 3l26 3l27 3l28 3l29 4ibb 4ibc 4ibd 4ibe 4ibf 4ibg 4ibi 4ibj 4ibk 4ije 4ijf 4ypi 4zta 4ztg 4zti

(-) Related Entries Specified in the PDB File

3fke ZAIRE EBOLA VP35 INTERFERON INHIBITORY DOMAIN
3l26
3l27
3l28
3l29
3l2a