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Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA
DOI:10.2210/pdb4ifd/pdb   NDB ID: NA2158
4IFD
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Hydrolase/rna
    Structure Weight: 438165.92
    Molecule: Exosome complex component RRP45
    Polymer: 1 Type: protein Length: 304
    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: 248
    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: 393
    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: 245
    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: 267
    Chains: E
    Mutation: V138I
    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
    Mutation: T75S, M161T
    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: 242
    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: 361
    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: 301
    Chains: I
    Organism: Saccharomyces cerevisiae S288c
    Gene Names: CSL4 SKI4 YNL232W N1154
    UniProtKB: Protein Feature View | Search PDB | P53859  
    Molecule: Exosome complex exonuclease DIS3
    Polymer: 10 Type: protein Length: 1003
    Chains: J
    EC#: 3.1.13    3.1.26   
    Mutation: D171N, D551N
    Organism: Saccharomyces cerevisiae S288c
    Gene Names: Gene View for DIS3 RRP44 YOL021C O2197
    UniProtKB: Protein Feature View | Search PDB | Q08162  
    Molecule: Exosome complex exonuclease RRP6
    Polymer: 11 Type: protein Length: 179
    Chains: K
    EC#: 3.1.13   
    Fragment: UNP RESIDUES 518-693
    Organism: Saccharomyces cerevisiae S288c
    Gene Names: RRP6 UNC733 YOR001W
    UniProtKB: Protein Feature View | Search PDB | Q12149  
    Molecule: RNA (45-MER)
    Polymer: 12 Type: rna Length: 45
    Chains: R
     
  •   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: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast Expression System: Escherichia coli  
    Polymer: 12
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Ligand Chemical Component Hide
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA2158
     
 
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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  •   MyPDB Personal Annotations Hide
     
  •   Deposition Summary Hide
    Authors:   Makino, D.L.,  Conti, E.

    Deposition:   2012-12-14
    Release:   2013-02-06
    Last Modified (REVDAT):   2013-11-13
     
  •   Revision History    Hide
    Mouse over text for details
    2013-11-13
    Citation
    2013-03-13
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   2.81
    R-Value: 0.185 (obs.)
    R-Free: 0.224
    Space Group: P 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 154.09 α = 90.00 
    b = 107.44 β = 110.63 
    c = 150.46 γ = 90.00