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Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA
DOI:10.2210/pdb4oo1/pdb   NDB ID: NA2898
4OO1
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Hydrolase/rna
    Structure Weight: 359659.30
    Molecule: Exosome complex component RRP45
    Polymer: 1 Type: protein Length: 305
    Chains: A
    Organism: Saccharomyces cerevisiae S288c
    Gene Names: RRP45 YDR280W D9954.1
    UniProtKB: Protein Feature View | Search PDB | Q05636  
    Molecule: Exosome complex component SKI6
    Polymer: 2 Type: protein Length: 250
    Chains: B
    Organism: Saccharomyces cerevisiae S288c
    Gene Names: SKI6 ECM20 RRP41 YGR195W G7587
    UniProtKB: Protein Feature View | Search PDB | P46948  
    Molecule: Exosome complex component RRP43
    Polymer: 3 Type: protein Length: 394
    Chains: C
    Organism: Saccharomyces cerevisiae S288c
    Gene Names: RRP43 YCR035C YCR35C YCR522
    UniProtKB: Protein Feature View | Search PDB | P25359  
    Molecule: Exosome complex component RRP46
    Polymer: 4 Type: protein Length: 225
    Chains: D
    Organism: Saccharomyces cerevisiae S288c
    Gene Names: RRP46 YGR095C
    UniProtKB: Protein Feature View | Search PDB | P53256  
    Molecule: Exosome complex component RRP42
    Polymer: 5 Type: protein Length: 269
    Chains: E
    Organism: Saccharomyces cerevisiae S288c
    Gene Names: RRP42 YDL111C
    UniProtKB: Protein Feature View | Search PDB | Q12277  
    Molecule: Exosome complex component MTR3
    Polymer: 6 Type: protein Length: 250
    Chains: F
    EC#: 3.1.13   
    Organism: Saccharomyces cerevisiae S288c
    Gene Names: MTR3 YGR158C G6676
    UniProtKB: Protein Feature View | Search PDB | P48240  
    Molecule: Exosome complex component RRP40
    Polymer: 7 Type: protein Length: 244
    Chains: G
    Organism: Saccharomyces cerevisiae S288c
    Gene Names: RRP40 YOL142W
    UniProtKB: Protein Feature View | Search PDB | Q08285  
    Molecule: Exosome complex component RRP4
    Polymer: 8 Type: protein Length: 363
    Chains: H
    Organism: Saccharomyces cerevisiae S288c
    Gene Names: RRP4 YHR069C
    UniProtKB: Protein Feature View | Search PDB | P38792  
    Molecule: Exosome complex component CSL4
    Polymer: 9 Type: protein Length: 296
    Chains: I
    Organism: Saccharomyces cerevisiae S288c
    Gene Names: CSL4 SKI4 YNL232W N1154
    UniProtKB: Protein Feature View | Search PDB | P53859  
    Molecule: Exosome complex exonuclease RRP6
    Polymer: 10 Type: protein Length: 560
    Chains: J
    EC#: 3.1.13   
    Mutation: D238N
    Organism: Saccharomyces cerevisiae S288c
    Gene Names: RRP6 UNC733 YOR001W
    UniProtKB: Protein Feature View | Search PDB | Q12149  
    Molecule: POLY A RNA
    Polymer: 11 Type: rna Length: 24
    Chains: S
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast Expression System: Escherichia coli  
    Polymer: 3
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast Expression System: Escherichia coli  
    Polymer: 4
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast Expression System: Escherichia coli  
    Polymer: 5
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast Expression System: Escherichia coli  
    Polymer: 6
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast Expression System: Escherichia coli  
    Polymer: 7
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast Expression System: Escherichia coli  
    Polymer: 8
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast Expression System: Escherichia coli  
    Polymer: 9
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast Expression System: Escherichia coli  
    Polymer: 10
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast Expression System: Escherichia coli  
    Polymer: 11
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    MES
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    MES C6 H13 N O4 S
    2-(N-MORPHOLINO)-ETHANESULFONIC ACID
    MG
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    MG Mg
    MAGNESIUM ION
    MPD
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    MPD C6 H14 O2
    (4S)-2-METHYL-2,4-PENTANEDIOL
    PO4
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    PO4 O4 P
    PHOSPHATE ION
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA2898
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
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  •   Deposition Summary Hide
    Authors:   Lima, C.D.,  Wasmuth, E.V.

    Deposition:   2014-01-29
    Release:   2014-07-02
    Last Modified (REVDAT):   2014-08-27
     
  •   Revision History    Hide
    Mouse over text for details
    2014-08-27
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    Resolution[Å]:   3.30
    R-Value: 0.229 (obs.)
    R-Free: 0.265
    Space Group: P 21 21 2
    Unit Cell:
      Length [Å] Angles [°]
    a = 193.29 α = 90.00 
    b = 200.08 β = 90.00 
    c = 97.40 γ = 90.00