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Crystal structure of T. thermophilus Argonaute complexed with DNA guide strand and 19-nt RNA target strand
DOI:10.2210/pdb3hm9/pdb   NDB ID: NA0119
3HM9
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Nucleic Acid Binding Protein/dna/rna
    Structure Weight: 89308.96
    Molecule: Argonaute
    Polymer: 1 Type: protein Length: 685
    Chains: A
    Organism: Thermus thermophilus HB27
    Gene Name: TT_P0026
    UniProtKB: Protein Feature View | Search PDB | Q746M7  
    Molecule: 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3'
    Polymer: 2 Type: dna Length: 21
    Chains: X
    Molecule: 5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3'
    Polymer: 3 Type: rna Length: 19
    Chains: Y
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Thermus thermophilus   Taxonomy   Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    3DLB  Same protein complexed with 10-nt DNA guide strand 
    3DLH  Same protein complexed with same DNA guide strand 
    3F73  Same protein complexed with same DNA guide strand and 20-nt RNA target with two mismatches. 
    3HGE  Mutant protein D546N complexed with same DNA guide and 20-nt RNA taget containing one nucleic acid bulge 
    3HJF  Mutant protein D546E complexed with same DNA guide and 15-nt RNA guide 
    3HK2  Mutant protein D478N complexed with same DNA guide and 19-nt RNA guide 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    MG
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    MG Mg
    MAGNESIUM ION
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA0119
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Biological assembly 1 generated by PISA (software)
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  •   Deposition Summary Hide
    Authors:   Wang, Y.,  Li, H.,  Sheng, G.,  Patel, D.J.

    Deposition:   2009-05-28
    Release:   2009-10-06
    Last Modified (REVDAT):   2011-07-13
     
  •   Revision History    Hide
    Mouse over text for details
    2011-07-13
    Source and taxonomy
    2011-07-13
    Flag residual B-value
    2011-07-13
    Refinement description
    2011-07-13
    Version format compliance
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   3.30
    R-Value: 0.239 (obs.)
    R-Free: 0.289
    Space Group: P 43 21 2
    Unit Cell:
      Length [Å] Angles [°]
    a = 111.92 α = 90.00 
    b = 111.92 β = 90.00 
    c = 175.55 γ = 90.00