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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This is version 2.0 of the entry. See complete history


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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XDH5
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase III subunit gamma/tauM, N, O, P177Thermus aquaticusMutation(s): 0 
Gene Names: dnaX_2dnaXBVI061214_00485
EC: 2.7.7.7
UniProt
Find proteins for A0A0M9ACL9 (Thermus aquaticus)
Explore A0A0M9ACL9 
Go to UniProtKB:  A0A0M9ACL9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M9ACL9
Protein Feature View
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  • Reference Sequence

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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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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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
BA [auth C],
FA [auth D],
T [auth A],
X [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
  • Version 2.0: 2022-04-20
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary