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 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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:  

  • 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 R ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III subunit delta
A, F
343Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: holA
EC: 2.7.7.7
Find proteins for P28630 (Escherichia coli (strain K12))
Go to UniProtKB:  P28630
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III subunit tau
B, C, D, G, H, I
395Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: dnaX (dnaZ, dnaZX)
EC: 2.7.7.7
Find proteins for P06710 (Escherichia coli (strain K12))
Go to UniProtKB:  P06710
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III subunit delta'
E, J
334Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: holB
EC: 2.7.7.7
Find proteins for P28631 (Escherichia coli (strain K12))
Go to UniProtKB:  P28631
Entity ID: 4
MoleculeChainsLengthOrganism
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,M20N/A
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*AP*TP*A)-3')L,N10N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, C, D, E, G, H, I, J
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

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Download CCD File 
B, C, D, G, H, I
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
B, C, D, G, H, I
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

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Download CCD File 
B, C, D, G, I
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 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 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 100.102α = 90.00
b = 219.104β = 90.00
c = 274.664γ = 90.00
Software Package:
Software NamePurpose
PHASESphasing
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-10-10
    Type: Database references