4IQJ

Structure of PolIIIalpha-Tauc-DNA complex suggests an atomic model of the replisome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.266 

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Literature

Structure of PolIIIalpha-Tauc-DNA complex suggests an atomic model of the replisome

Liu, B.Lin, J.Steitz, T.A.

(2013) Structure 21: 658-664

  • DOI: 10.1016/j.str.2013.02.002
  • Primary Citation of Related Structures:  
    4IQJ

  • PubMed Abstract: 
  • The C-terminal domain (CTD) of the τ subunit of the clamp loader (τc) binds to both the DnaB helicase and the DNA polymerase III α subunit (PolIIIα), and determines their relative positions and orientations on the leading and lagging strands. Here, we present a 3 ...

    The C-terminal domain (CTD) of the τ subunit of the clamp loader (τc) binds to both the DnaB helicase and the DNA polymerase III α subunit (PolIIIα), and determines their relative positions and orientations on the leading and lagging strands. Here, we present a 3.2 Å resolution structure of Thermus aquaticus PolIIIα in complex with τc and a DNA substrate. The structure reveals that the CTD of τc interacts with the CTD of PolIIIα through its C-terminal helix and the adjacent loop. Additionally, in this complex PolIIIα displays an open conformation that includes the reorientations of the oligonucleotide-binding fold and the thumb domain, which may be an indirect result of crystal packing due to the presence of the τc. Nevertheless, the position of the τc on PolIIIα allows us to suggest an approximate model for how the PolIIIα is oriented and positioned on the DnaB helicase.


    Related Citations: 
    • The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases.
      Bailey, S., Wing, R.A., Steitz, T.A.
      (2006) Cell 126: 893
    • Insights into the replisome from the structure of a ternary complex of the DNA polymerase III alpha-subunit.
      Wing, R.A., Bailey, S., Steitz, T.A.
      (2008) J Mol Biol 382: 859

    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase III subunit alphaI [auth A], J [auth B], K [auth C], L [auth D]1220Thermus aquaticusMutation(s): 0 
Gene Names: dnaE
EC: 2.7.7.7
UniProt
Find proteins for Q9XDH5 (Thermus aquaticus)
Explore Q9XDH5 
Go to UniProtKB:  Q9XDH5
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
C-terminal domain of the DNA polymerase III subunit tauM, N, O, P177Thermus aquaticusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*CP*GP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*A)-3')A [auth E], C [auth G], G [auth K]20synthetic construct
    Protein Feature View
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    • Reference Sequence
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    Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*GP*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*CP*G)-3')B [auth F], D [auth H], F [auth J], H [auth L]28synthetic construct
    Protein Feature View
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    • Reference Sequence
    Find similar nucleic acids by:  (by identity cutoff)  |  Structure
    Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*CP*GP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*(DOC))-3')E [auth I]21synthetic construct
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    DOC (Subject of Investigation/LOI)
    Query on DOC

    Download Ideal Coordinates CCD File 
    Q [auth I]2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
    C9 H14 N3 O6 P
    RAJMXAZJKUGYGW-POYBYMJQSA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    AA [auth C] , BA [auth C] , DA [auth D] , EA [auth D] , FA [auth D] , R [auth A] , S [auth A] , T [auth A] , 
    AA [auth C],  BA [auth C],  DA [auth D],  EA [auth D],  FA [auth D],  R [auth A],  S [auth A],  T [auth A],  V [auth B],  W [auth B],  X [auth B],  Z [auth C]
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    CA [auth C], GA [auth D], U [auth A], Y [auth B]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.20 Å
    • R-Value Free: 0.305 
    • R-Value Work: 0.264 
    • R-Value Observed: 0.266 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 188.53α = 90
    b = 94.97β = 89.97
    c = 204.08γ = 90
    Software Package:
    Software NamePurpose
    BOSdata collection
    PHASERphasing
    PHENIXmodel building
    REFMACrefinement
    iMOSFLMdata reduction
    SCALAdata scaling
    PHENIXphasing

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2013-03-13
      Type: Initial release
    • Version 1.1: 2013-06-19
      Changes: Database references