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(-) Description

Title :  STRUCTURAL BASIS FOR MARBURG VIRUS VP35 MEDIATE IMMUNE EVASION MECHANISMS
 
Authors :  P. Ramanan, D. M. Borek, Z. Otwinowski, D. W. Leung, G. K. Amarasinghe
Date :  07 Aug 12  (Deposition) - 28 Nov 12  (Release) - 26 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A (1x),B (1x),C (1x),D (1x),E (1x),F (1x)
Keywords :  Protein-Rna Complex, Vp35, Ifn Inhibitor, Rna Binding Protein, Interferon Antagonism, Double Stranded Rna, Transcription, Viral Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Ramanan, M. R. Edwards, R. S. Shabman, D. W. Leung, A. C. Endlich-Frazier, D. M. Borek, Z. Otwinowski, G. Liu, J. Huh, C. F. Basler, G. K. Amarasinghe
Structural Basis For Marburg Virus Vp35-Mediated Immune Evasion Mechanisms.
Proc. Natl. Acad. Sci. Usa V. 109 20661 2012
PubMed-ID: 23185024  |  Reference-DOI: 10.1073/PNAS.1213559109

(-) Compounds

Molecule 1 - SHORT PALINDROMIC RNA AGACAGCAUAUGCUGUCU
    ChainsE, F
    EngineeredYES
    Other DetailsIDT DNA
    SyntheticYES
 
Molecule 2 - POLYMERASE COFACTOR VP35
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypeCOLE1
    FragmentUNP RESIDUES 200-329
    GenePOLYMERASE COFACTOR VP35, VP35
    MutationYES
    Organism CommonMARV
    Organism ScientificLAKE VICTORIA MARBURGVIRUS
    Organism Taxid33728
    StrainPOPP-67

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A (1x)B (1x)C (1x)D (1x)E (1x)F (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric Unit (3, 19)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3MG11Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREC E:17 , U E:18BINDING SITE FOR RESIDUE MG E 101
02AC2SOFTWAREA E:1 , U E:18BINDING SITE FOR RESIDUE MG E 102
03AC3SOFTWAREU E:16BINDING SITE FOR RESIDUE MG E 103
04AC4SOFTWAREA F:10 , U F:11BINDING SITE FOR RESIDUE MG F 101
05AC5SOFTWAREC F:13 , U F:14 , HOH F:210BINDING SITE FOR RESIDUE MG F 102
06AC6SOFTWAREU F:14 , G F:15BINDING SITE FOR RESIDUE MG F 103
07AC7SOFTWARELYS A:287 , GLU A:320 , GLU C:320BINDING SITE FOR RESIDUE MG A 401
08AC8SOFTWAREILE A:284 , ARG A:285BINDING SITE FOR RESIDUE EDO A 402
09AC9SOFTWAREASN A:225 , PRO A:293 , ARG A:294 , PRO A:295 , HOH A:588 , HOH B:570BINDING SITE FOR RESIDUE EDO A 403
10BC1SOFTWARELEU B:221 , GLY B:223 , HOH B:504 , HOH B:569BINDING SITE FOR RESIDUE MG B 401
11BC2SOFTWARELYS B:241BINDING SITE FOR RESIDUE CL B 404
12BC3SOFTWAREHIS A:198 , GLU A:201 , ALA B:302 , ARG B:325 , HOH B:514BINDING SITE FOR RESIDUE EDO B 405
13BC4SOFTWAREHOH A:593 , ARG C:301 , LYS C:328 , A E:8BINDING SITE FOR RESIDUE MG C 401
14BC5SOFTWAREPHE C:218 , LEU C:221 , GLY C:223 , HIS C:229 , HOH C:554BINDING SITE FOR RESIDUE MG C 402
15BC6SOFTWAREARG C:285BINDING SITE FOR RESIDUE CL C 403
16BC7SOFTWAREARG C:285 , HOH C:501BINDING SITE FOR RESIDUE EDO C 404
17BC8SOFTWAREPHE D:289 , GLN D:290BINDING SITE FOR RESIDUE MG D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GHL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GHL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GHL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GHL)

(-) Exons   (0, 0)

(no "Exon" information available for 4GHL)

(-) 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:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhh....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....eee..hhhhhhhhhhh.ee......hhhh.eeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ghl A 198 HMEETFSKPNLSAKDLALLLFTHLPGNNTPFHILAQVLSKIAYKSGKSGAFLDAFHQILSEGENAQAALTRLSRTFDAFMGVVPPVIRVKNFQTVPRPCQKSLRAVPPNPTIDKGWVCVYSSEQGETRALKI 329
                                   207       217       227       237       247       257       267       277       287       297       307       317       327  

Chain B from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh......hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....eee..hhhhhhhhhhh.ee......hhhh.eeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ghl B 208 LSAKDLALLLFTHLPGNNTPFHILAQVLSKIAYKSGKSGAFLDAFHQILSEGENAQAALTRLSRTFDAFMGVVPPVIRVKNFQTVPRPCQKSLRAVPPNPTIDKGWVCVYSSEQGETRALKI 329
                                   217       227       237       247       257       267       277       287       297       307       317       327  

Chain C from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....eee.......hhhhhh.ee......hhhh.eeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ghl C 208 LSAKDLALLLFTHLPGNNTPFHILAQVLSKIAYKSGKSGAFLDAFHQILSEGENAQAALTRLSRTFDAFMGVVPPVIRVKNFQTVPRPCQKSLRAVPPNPTIDKGWVCVYSSEQGETRALKI 329
                                   217       227       237       247       257       267       277       287       297       307       317       327  

Chain D from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....eeee......hhhhhh.ee......hhhh.eeeeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ghl D 208 LSAKDLALLLFTHLPGNNTPFHILAQVLSKIAYKSGKSGAFLDAFHQILSEGENAQAALTRLSRTFDAFMGVVPPVIRVKNFQTVPRPCQKSLRAVPPNPTIDKGWVCVYSSEQGETRALKI 329
                                   217       227       237       247       257       267       277       287       297       307       317       327  

Chain E from PDB  Type:RNA  Length:18
                                                  
                 4ghl E   1 AGACAGCAUAUGCUGUCU  18
                                    10        

Chain F from PDB  Type:RNA  Length:18
                                                  
                 4ghl F   1 AGACAGCAUAUGCUGUCU  18
                                    10        

   Legend:   → Mismatch (orange background)
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  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 4GHL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GHL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GHL)

(-) Gene Ontology  (3, 3)

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(-) Related Entries Specified in the PDB File

3fke 3l25 3l26 3l27 3l28 3l29