3GLG

Crystal Structure of a Mutant (gammaT157A) E. coli Clamp Loader Bound to Primer-Template DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

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Literature

The mechanism of ATP-dependent primer-template recognition by a clamp loader complex.

Simonetta, K.R., Kazmirski, S.L., Goedken, E.R., Cantor, A.J., Kelch, B.A., McNally, R., Seyedin, S.N., Makino, D.L., O'Donnell, M., Kuriyan, J.

(2009) Cell 137: 659-671

  • DOI: 10.1016/j.cell.2009.03.044
  • Primary Citation of Related Structures:  
    3GLF, 3GLG, 3GLH, 3GLI

  • PubMed Abstract: 

    • Clamp loaders load sliding clamps onto primer-template DNA. The structure of the E. coli clamp loader bound to DNA reveals the formation of an ATP-dependent spiral of ATPase domains that tracks only the template strand, allowing recognition of both RNA and DNA primers ...

    Clamp loaders load sliding clamps onto primer-template DNA. The structure of the E. coli clamp loader bound to DNA reveals the formation of an ATP-dependent spiral of ATPase domains that tracks only the template strand, allowing recognition of both RNA and DNA primers. Unlike hexameric helicases, in which DNA translocation requires distinct conformations of the ATPase domains, the clamp loader spiral is symmetric and is set up to trigger release upon DNA recognition. Specificity for primed DNA arises from blockage of the end of the primer and accommodation of the emerging template along a surface groove. A related structure reveals how the psi protein, essential for coupling the clamp loader to single-stranded DNA-binding protein (SSB), binds to the clamp loader. By stabilizing a conformation of the clamp loader that is consistent with the ATPase spiral observed upon DNA binding, psi binding promotes the clamp-loading activity of the complex.

    Organizational Affiliation: 

    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase III subunit deltaA, F343Escherichia coli K-12Mutation(s): 0 
Gene Names: holA, b0640, JW0635
EC: 2.7.7.7
UniProt
Find proteins for P28630 (Escherichia coli (strain K12))
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Go to UniProtKB:  P28630
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UniProt GroupP28630
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase III subunit tau
B, C, D, G, H, I
B, C, D, G, H, I
395Escherichia coli K-12Mutation(s): 1 
Gene Names: dnaX, dnaZ, dnaZX, b0470, JW0459
EC: 2.7.7.7
UniProt
Find proteins for P06710 (Escherichia coli (strain K12))
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Go to UniProtKB:  P06710
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UniProt GroupP06710
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase III subunit delta'E, J334Escherichia coli K-12Mutation(s): 0 
Gene Names: holB, b1099, JW1085
EC: 2.7.7.7
UniProt
Find proteins for P28631 (Escherichia coli (strain K12))
Explore P28631 
Go to UniProtKB:  P28631
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UniProt GroupP28631
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*GP*GP*CP*CP*AP*G)-3')K, M 20N/A
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*AP*TP*A)-3')L, N 10N/A
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download Ideal Coordinates CCD File 
BA [auth G],
FA [auth H],
JA [auth I],
O [auth B],
S [auth C],
BA [auth G],
FA [auth H],
JA [auth I],
O [auth B],
S [auth C],
W [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
BEF
Query on BEF
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CA [auth G],
IA [auth I],
KA [auth I],
P [auth B],
T [auth C],
CA [auth G],
IA [auth I],
KA [auth I],
P [auth B],
T [auth C],
X [auth D]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K		 Ligand Interaction
ZN
Query on ZN
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AA [auth E],
EA [auth G],
HA [auth H],
MA [auth I],
NA [auth J],
AA [auth E],
EA [auth G],
HA [auth H],
MA [auth I],
NA [auth J],
R [auth B],
V [auth C],
Z [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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DA [auth G],
GA [auth H],
LA [auth I],
Q [auth B],
U [auth C],
DA [auth G],
GA [auth H],
LA [auth I],
Q [auth B],
U [auth C],
Y [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.102α = 90
b = 219.104β = 90
c = 274.664γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-10-10
    Changes: Database references
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations